{
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        "bash_script_MD5": "f281c99b69baed5d8e94154dbcf0ad16",
        "running_time": "Fri_Oct__4_08:31:40_CDT_2019"
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        "percentage_of_non-redundant_uniquely_mapped_reads_in_chrX": 0.0447,
        "percentage_of_non-redundant_uniquely_mapped_reads_in_chrY": 0.0014,
        "Percentage_of_non-redundant_uniquely_mapped_reads_in_autosome": {"chr1": 0.0849, "chr2": 0.0839, "chr3": 0.068, "chr4": 0.0598, "chr5": 0.0605, "chr6": 0.0579, "chr7": 0.0541, "chr8": 0.0512, "chr9": 0.042, "chr10": 0.0494, "chr11": 0.0504, "chr12": 0.0473, "chr13": 0.0308, "chr14": 0.0319, "chr15": 0.0302, "chr16": 0.0319, "chr17": 0.0335, "chr18": 0.0265, "chr19": 0.0248, "chr20": 0.0266, "chr21": 0.0138, "chr22": 0.0165}
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    "peak_analysis": {
        "peak_calling_software": "macs2",
        "peak_calling_parameters": "--keep-dup 1000 --nomodel --shift 0 --extsize 150",
        "peak_threshold_parameter": "qvaule",
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    }
  },
  "ENCODE PE refernce": {
    "data information": {
        "pipe version": "V3",
        "Docker tag": "target",
        "genome": "mm10",
        "read type": "Paired-end data"
    },
    "mapping stats": {
        "alignment program": "bwa",
        "alignment program version": "0.7.16a",
        "alignment program parameters": "bwa men",
        "post alignment program": "methylQA",
        "post alignment program version": "0.1.9",
        "post alignment program parameters": "methylQA atac",
        "total reads": [53521173,52841837,49568333,52179809,49691764,51407232,35924683,48416233,43503968,53935170,43919645,42278369,47548519,41466599,86375299,48785458,52082703,53078621,44189469,42364518,44562754,53140917,40755321,83791512,57818671,55554407,58056975,56463898,49454428,44646781,42044382,49443834,46776162,38328988,38505907,68272995,66315169,48348502,70091736,54588699,64152873,51902255,74018175,53219421,55307973,51449827,60200454,43550852,52300091,37376936,47681374,42220415,63001963,55360933],
        "mapped reads": [43153580,42352477,40229473,42084338,40291437,42716896,28866333,39886059,34766414,43002187,35234920,34848824,39069214,34125943,69416398,38266364,41765449,42472011,35204142,33813586,39790102,48179030,36332407,71257866,49597633,47494669,49211981,47609742,40952588,36620751,33314063,39567448,35867421,30385187,29796011,56853075,55132909,39816744,55306693,42147170,49206590,40035934,63486809,44917615,47228932,44222865,44153141,32173136,39219035,26981011,34913406,30567779,53595288,45140181],
        "uniquely mapped reads": [42735187,41950396,39892521,41671318,40023928,42419895,28655248,39664818,34533848,42699479,35029567,34684686,38882460,33902845,68757933,37885873,41382639,42061841,34913489,33524222,39513192,47902342,36053467,70701654,49250461,47163021,48894920,47293755,40607252,36297159,33036123,39224311,35600242,30109011,29557977,56293216,54708676,39509001,54921964,41772135,48755362,39678322,62946399,44506281,46848675,43877034,43882564,31955516,38963822,26790046,34708259,30315741,53112493,44697439],
        "non-redundant mapped reads": [39045290,38027740,36822477,37914795,35681662,38482560,25640256,35563680,30468442,35964313,29983078,29486250,34677104,28328824,59970088,33388823,37659611,37990545,31206803,30136814,35594598,42508046,32708309,56716944,43786201,41405826,42048361,39994718,33434773,29290122,29440814,33946966,31312483,27073004,25517372,45645909,41507394,29033906,38777600,27948067,41966430,34194715,55550516,39160672,40919632,38422470,38791422,29171658,35229878,23537123,29178926,25560630,48237836,38811180],
        "useful reads": [38286495,37046058,36092973,37322817,34664807,37588382,25198225,34770694,29541806,34877663,28883250,28465741,33727855,27478975,58755388,32416527,36901151,37180635,30266809,29333834,34757288,41636024,32125668,55044789,42760084,40230858,40522043,38435668,32166278,27815309,28378414,32719725,30043071,26312383,24306859,44010703,39473963,27272092,36609370,25903627,40664825,32947367,54382844,38030358,39852634,37534831,37743991,28338484,34346943,22692393,28743123,24922703,47262684,37207722],
        "useful single ends": [76572990,74092116,72185946,74645634,69329614,75176764,50396450,69541388,59083612,69755326,57766500,56931482,67455710,54957950,117510776,64833054,73802302,74361270,60533618,58667668,69514576,83272048,64251336,110089578,85520168,80461716,81044086,76871336,64332556,55630618,56756828,65439450,60086142,52624766,48613718,88021406,78947926,54544184,73218740,51807254,81329650,65894734,108765688,76060716,79705268,75069662,75487982,56676968,68693886,45384786,57486246,49845406,94525368,74415444]
    },
    "library complexity": {
        "after alignment PCR duplicates percentage": [0.0669999999999999,0.0590000000000001,0.0580000000000001,0.077,0.071,0.0649999999999999,0.096,0.081,0.081,0.117,0.092,0.105,0.074,0.134,0.098,0.083,0.071,0.075,0.071,0.074,0.071,0.088,0.079,0.124,0.083,0.082,0.075,0.081,0.123,0.111,0.0590000000000001,0.078,0.054,0.0669999999999999,0.0639999999999999,0.11,0.115,0.136,0.155,0.179,0.09,0.083,0.087,0.079,0.092,0.098,0.081,0.0580000000000001,0.069,0.086,0.153,0.141,0.0639999999999999,0.056]
    },
    "peak analysis": {
        "peak calling software": "macs2",
        "peak calling parameters": "--keep-dup 1000 --nomodel --shift 0 --extsize 150",
        "peak threshold parameter": "qvaule",
        "peak threshold": 0.01,
        "reads percentage under peaks": [0.1292,0.1194,0.1715,0.0954,0.1865,0.2143,0.1892,0.2739,0.1869,0.1951,0.2468,0.3124,0.376,0.2318,0.1301,0.1031,0.1242,0.1263,0.1443,0.1407,0.1777,0.2005,0.1508,0.1709,0.2131,0.2143,0.251,0.2289,0.1848,0.151,0.1377,0.1413,0.1771,0.1138,0.1571,0.1233,0.2416,0.1962,0.4163,0.3119,0.2875,0.319,0.1761,0.1324,0.183,0.1939,0.1985,0.1781,0.1754,0.1624,0.1951,0.1016,0.1347,0.1694],
        "reads number under peaks": [9811438,8774097,12265101,7065600,12796830,15947809,9432387,18834750,10926114,13473224,14096158,17550145,24926840,12577431,15169277,6629860,9084049,9307498,8645913,8176337,12230668,16525586,9593749,18636859,18014767,17054844,20096977,17386923,11681493,8269024,7742949,9158421,10534062,5929255,7531003,10730541,18703706,10522241,29572680,15697637,23050218,20696530,18984054,9978365,14435791,14406726,14822352,9985987,11925204,7290002,11093907,5020171,12607822,12463879],
        "peaks number in promoter regions": [14477,14145,14868,13733,14744,15237,14200,15584,14510,15211,15167,15650,16473,15521,14686,13440,14154,14226,14242,14038,15208,15512,14874,16104,16799,16911,17311,16685,14850,13967,15366,15635,16277,15258,13886,13856,13595,13099,15925,14592,17238,17159,15520,14358,15490,15269,14747,14510,14806,13866,14716,13077,15707,16417],
        "peaks number in non-promoter regions": [33335,30617,43721,24189,50064,53274,37693,63859,43847,52738,59340,68210,86462,57548,37472,24065,31615,32290,31700,29608,47013,55366,42303,57261,57169,60123,67570,59511,43994,36843,40786,43070,53779,34782,31055,28790,33074,27953,60339,45326,78165,74463,47085,31465,48264,46018,44445,35400,40301,28548,39066,18454,46668,54210]
    },
    "enrichment": {
        "enrichment ratio in coding promoter regions": [14.136,12.296,16.16,8.18,8.513,14.933,8.581,9.32,11.5,12.383,10.257,11.688,11.221,12.094,6.971,12.52,8.317,10.669,8.456,11.689,11.863,11.185,17.456,21.05,11.468,11.929,6.977,10.024,9.969,12.054,6.788,20.625,8.156,11.148,8.239,9.982,9.362,14.347,9.821,10.313,13.651,13.208,10.01,25.296,11.727,8.301,13.642,8.733,7.846,11.113,7.224,8.14,13.448,16.25],
        "subsampled 10M enrichment ratio": [20.0751960291,16.9365522834,28.5592416042,16.5750076566,15.6160587689,17.8926912918,17.2628079078,17.9767092513,17.5390101683,17.6032387948,19.2296282833,17.7392147705,16.9579954453,16.8918353327,14.9166314269,18.8505432093,18.0756918468,16.4321073588,15.5357255478,17.426875664,17.7421222561,16.8158703756,20.0085220044,22.2452856369,16.2795459894,18.5311481308,15.9968380655,18.0918133729,16.522756908,17.2040802699,14.5428255822,27.2038806667,14.4630142898,16.2649026692,14.8475900548,16.4251850656,16.1057058162,18.1814386273,16.9892634495,15.9255873558,24.954998221,19.210203775,16.1552163426,29.8046802599,17.1783351364,14.5727165738,18.7300320681,15.4182600148,14.7647221963,17.2786818249,14.2266656533,14.67821709,19.4827391372,21.3672015923],
        "percentage of background RPKM larger than 0.3777": [0.1912,0.2199,0.1426,0.2792,0.0829,0.0754,0.1392,0.0408,0.0754,0.0573,0.0376,0.02,0.0152,0.0591,0.2146,0.2441,0.1914,0.2066,0.1376,0.1606,0.0615,0.0422,0.1621,0.0699,0.0533,0.0491,0.0281,0.0433,0.1091,0.1455,0.1327,0.1118,0.0856,0.1363,0.16,0.2046,0.0866,0.106,0.0265,0.1336,0.069,0.0542,0.1241,0.1873,0.1068,0.0887,0.0587,0.0855,0.0722,0.1198,0.0634,0.2114,0.1007,0.1295]
    }
  }
} 
