{"text_format":"3","workbook":"xls","n_sheets":1,"sheets":["data characterization"],"read":"whole","date_system":"1900","formulas":"cached_only"}

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[" # The number of TP and FP variant calls in 5 individual variant call-sets identified by GATK HaplotypeCaller, Mutect2, and Varscan2, and DeepVariant"]
[]
["Depth","software","patient","TP (Total)","FP (Total)","TP (High Frequency)","FP (High Frequency)","TP (Low Frequency)","FP (Low Frequency)","TP (hard-to-detect)","FP (hard-to-detect)","TP (easy-to-detect)","FP (easy-to-detect)","TP (Coding)","FP (Coding)","TP (Non-Coding)","FP (Non-Coding)","Average TP (total)","Average FP (total)","Average TP (High Frequency)","Average FP (High Frequency)","Average TP (Low Frequency)","Average FP (Low Frequency)","Average TP (hard-to-detect)","Average FP (hard-to-detect)","Average TP (easy-to-detect)","Average FP (easy-to-detect)","Average TP (coding)","Average FP (coding)","Average TP (noncoding)","Average FP (noncoding)","FP/All(Low-frequency) %","FP/All(hard-to-detect) %","FP/All(coding) %","TP/All(Low-frequency) %","TP/All(Hard-to-detect) %","TP/All(coding) %"]
["30X","gatk","HG001",3685747,6124,3683038,3223,2709,2901,169738,3744,3516007,2380,69308,188,3616437,5936,{"v":3507543.8,"d":"3507544"},{"v":7077.8,"d":"7078"},{"v":3504630.6,"d":"3504631"},{"v":3240.2,"d":"3240"},{"v":2913.2,"d":"2913"},{"v":3837.6,"d":"3838"},{"v":153584.8,"d":"153585"},{"v":4408.6,"d":"4409"},3353957,{"v":2669.2,"d":"2669"},66541,160,{"v":3441000.8,"d":"3441001"},{"v":6917.8,"d":"6918"},{"v":54.220237927039484,"d":"54.22"},{"v":62.28771652208314,"d":"62.29"},{"v":2.2605894486987483,"d":"2.26"},{"v":0.08305527075670444,"d":"0.08"},{"v":4.378701915968613,"d":"4.38"},{"v":1.8970835928455652,"d":"1.90"}]
["30X","gatk","HG003",3452320,10376,3447849,4412,4471,5964,195304,8219,3257014,2157,64993,133,3387325,10243]
["30X","gatk","HG004",3490217,9798,3486664,3775,3553,6023,126383,4657,3363832,5141,65694,158,3424521,9640]
["30X","gatk","HG006",3445646,4677,3443749,2433,1897,2244,127908,2646,3317736,2031,66213,168,3379431,4509]
["30X","gatk","HG007",3463789,4414,3461853,2358,1936,2056,148591,2777,3315196,1637,66497,153,3397290,4261]
["30X","mutect2","HG001",3664317,38171,3660935,7862,3382,30309,177451,36007,3486864,2164,68886,817,3595429,37354,{"v":3486692.4,"d":"3486692"},{"v":59133.4,"d":"59133"},{"v":3483186.8,"d":"3483187"},{"v":16125.6,"d":"16126"},{"v":3505.6,"d":"3506"},{"v":43007.8,"d":"43008"},{"v":160133.6,"d":"160134"},{"v":56254.2,"d":"56254"},{"v":3326556.8,"d":"3326557"},{"v":2879.2,"d":"2879"},{"v":66122.8,"d":"66123"},{"v":1132.8,"d":"1133"},{"v":3420567.6,"d":"3420568"},{"v":58000.6,"d":"58001"},{"v":72.73013220954655,"d":"72.73"},{"v":95.13100887146689,"d":"95.13"},{"v":1.9156686407343395,"d":"1.92"},{"v":0.10054227898050312,"d":"0.10"},{"v":4.592710611759507,"d":"4.59"},{"v":1.8964345099295308,"d":"1.90"}]
["30X","mutect2","HG003",3432431,96580,3427290,32772,5141,63808,163729,92879,3268700,3701,64584,1602,3367845,94978]
["30X","mutect2","HG004",3469785,94605,3465511,28213,4274,66392,157253,90277,3312530,4328,65272,1578,3404511,93027]
["30X","mutect2","HG006",3424340,35242,3422003,5952,2337,29290,151051,33154,3273287,2088,65798,849,3358540,34393]
["30X","mutect2","HG007",3442589,31069,3440195,5829,2394,25240,151184,28954,3291403,2115,66074,818,3376513,30251]
["30X","varscan","HG001",3677341,31937,3672817,15578,4524,16359,15486,12097,3661853,19840,69148,970,3608191,30967,{"v":3505952.2,"d":"3505952"},{"v":51263.6,"d":"51264"},{"v":3501722.8,"d":"3501723"},{"v":16730.4,"d":"16730"},{"v":4229.4,"d":"4229"},{"v":34533.2,"d":"34533"},11207,{"v":18480.2,"d":"18480"},{"v":3494743.2,"d":"3494743"},{"v":32783.4,"d":"32783"},{"v":66456.2,"d":"66456"},{"v":994.2,"d":"994"},3439494,{"v":50269.4,"d":"50269"},{"v":67.36397755912577,"d":"67.36"},{"v":36.04936055992946,"d":"36.05"},{"v":1.9393877917274638,"d":"1.94"},{"v":0.120634844935992,"d":"0.12"},{"v":0.3196565655724374,"d":"0.32"},{"v":1.8955260687958428,"d":"1.90"}]
["30X","varscan","HG003",3457522,77041,3453102,21311,4420,55730,12146,27653,3445374,49388,64997,1047,3392523,75994]
["30X","varscan","HG004",3496233,86088,3491999,20933,4234,65155,9225,29531,3487006,56557,65703,1274,3430528,84814]
["30X","varscan","HG006",3440323,30659,3436376,12911,3947,17748,9629,11717,3430692,18942,66064,835,3374257,29824]
["30X","varscan","HG007",3458342,30593,3454320,12919,4022,17674,9549,11403,3448791,19190,66369,845,3391971,29748]
["30X","deepvariant","HG001",3690084,2075,3685559,1429,4525,646,57975,1176,3632107,899,69391,37,3620691,2038,{"v":3515932.8,"d":"3515933"},1595,{"v":3512416.6,"d":"3512417"},{"v":1103.8,"d":"1104"},{"v":3516.2,"d":"3516"},{"v":491.2,"d":"491"},{"v":83293.8,"d":"83294"},886,3432637,709,{"v":66626.6,"d":"66627"},{"v":25.2,"d":"25"},{"v":3449304.2,"d":"3449304"},{"v":1569.8,"d":"1570"},{"v":30.796238244514107,"d":"30.80"},{"v":55.54858934169279,"d":"55.55"},{"v":1.5799373040752351,"d":"1.58"},{"v":0.10000759969018747,"d":"0.10"},{"v":2.369039800214498,"d":"2.37"},{"v":1.894991789940803,"d":"1.89"}]
["30X","deepvariant","HG003",3469612,2210,3465244,1469,4368,741,140128,1146,3329482,1064,65133,36,3404477,2174]
["30X","deepvariant","HG004",3505402,1785,3501857,1243,3545,542,130548,1008,3374852,777,65826,17,3439574,1768]
["30X","deepvariant","HG006",3448242,981,3445681,674,2561,307,42911,531,3405329,450,66248,23,3381992,958]
["30X","deepvariant","HG007",3466324,924,3463742,704,2582,220,44907,569,3421415,355,66535,13,3399787,911]
["50X","gatk","HG001",3689674,7490,3688997,3812,677,3678,131224,4441,3558448,3049,69379,272,3620293,7218,{"v":3512558.4,"d":"3512558"},7087,3510972,{"v":2967.8,"d":"2968"},{"v":1586.4,"d":"1586"},{"v":4119.2,"d":"4119"},{"v":127825.4,"d":"127825"},{"v":3720.2,"d":"3720"},3384731,{"v":3366.8,"d":"3367"},{"v":66593.8,"d":"66594"},{"v":177.8,"d":"178"},{"v":3445962.6,"d":"3445963"},{"v":6909.2,"d":"6909"},{"v":58.12332439678284,"d":"58.12"},{"v":52.49329758713136,"d":"52.49"},{"v":2.5088189643008327,"d":"2.51"},{"v":0.045163661905236935,"d":"0.05"},{"v":3.6390988625833876,"d":"3.64"},{"v":1.8958784547915017,"d":"1.90"}]
["50X","gatk","HG003",3463801,9882,3462001,3346,1800,6536,117505,4633,3346294,5249,65100,147,3398699,9735]
["50X","gatk","HG004",3500005,8948,3498388,2871,1617,6077,110995,4297,3389008,4651,65781,146,3434222,8802]
["50X","gatk","HG006",3445580,4689,3443681,2445,1899,2244,142053,2704,3303525,1985,66213,169,3379365,4520]
["50X","gatk","HG007",3463732,4426,3461793,2365,1939,2061,137350,2526,3326380,1900,66496,155,3397234,4271]
["50X","mutect2","HG001",3666790,60433,3665574,9426,1216,51007,145449,54336,3521339,6097,68935,1252,3597853,59181,{"v":3490935.8,"d":"3490936"},{"v":68915.4,"d":"68915"},3489483,{"v":10929.8,"d":"10930"},{"v":1452.8,"d":"1453"},{"v":57985.6,"d":"57986"},{"v":132955.6,"d":"132956"},{"v":62252.8,"d":"62253"},{"v":3357978.2,"d":"3357978"},{"v":6662.6,"d":"6663"},66170,1345,{"v":3424763.8,"d":"3424764"},{"v":67570.4,"d":"67570"},{"v":84.14026473037957,"d":"84.14"},{"v":90.33220441294688,"d":"90.33"},{"v":1.951668277337141,"d":"1.95"},{"v":0.04161634825825213,"d":"0.04"},{"v":3.808597000607689,"d":"3.81"},{"v":1.8954813752125579,"d":"1.90"}]
["50X","mutect2","HG003",3441064,90765,3438702,16483,2362,74282,131440,83272,3309622,7493,64666,1397,3376396,89368]
["50X","mutect2","HG004",3477190,92761,3475010,14520,2180,78241,128882,84557,3348306,8204,65342,1572,3411846,91189]
["50X","mutect2","HG006",3425729,53999,3424949,7126,780,46873,129870,48264,3295857,5735,65814,1259,3359913,52740]
["50X","mutect2","HG007",3443906,46619,3443180,7094,726,39525,129137,40835,3314767,5784,66093,1245,3377811,45374]
["50X","varscan","HG001",3687962,83111,3683306,12826,4656,70285,5044,34745,3682916,48366,69369,2185,3618591,80926,{"v":3514256.2,"d":"3514256"},{"v":159441.8,"d":"159442"},{"v":3510254.8,"d":"3510255"},{"v":12339.6,"d":"12340"},{"v":4001.4,"d":"4001"},{"v":147102.2,"d":"147102"},{"v":4260.6,"d":"4261"},{"v":58290.2,"d":"58290"},{"v":3509993.6,"d":"3509994"},{"v":101151.6,"d":"101152"},66593,2916,{"v":3447661.2,"d":"3447661"},{"v":156525.8,"d":"156526"},{"v":92.26074969048267,"d":"92.26"},{"v":36.558919931912456,"d":"36.56"},{"v":1.828880506868337,"d":"1.83"},{"v":0.11386193186484243,"d":"0.11"},{"v":0.12123767256221818,"d":"0.12"},{"v":1.8949397570613986,"d":"1.89"}]
["50X","varscan","HG003",3468139,259605,3463844,14959,4295,244646,4647,90708,3463490,168897,65117,3580,3403020,256025]
["50X","varscan","HG004",3504302,294617,3500180,14016,4122,280601,4350,100130,3499950,194487,65817,4501,3438483,290116]
["50X","varscan","HG006",3446424,79596,3442925,9944,3499,69652,3668,32852,3442754,46744,66184,2136,3380238,77460]
["50X","varscan","HG007",3464454,80280,3461019,9953,3435,70327,3594,33016,3460858,47264,66478,2178,3397974,78102]
["50X","deepvariant","HG001",3691190,1056,3689633,886,1557,170,34247,844,3656941,212,69406,19,3621782,1037,{"v":3517026.4,"d":"3517026"},{"v":849.6,"d":"850"},{"v":3515880.2,"d":"3515880"},{"v":681.4,"d":"681"},{"v":1146.2,"d":"1146"},{"v":168.2,"d":"168"},{"v":73958.6,"d":"73959"},636,{"v":3443065.8,"d":"3443066"},{"v":213.6,"d":"214"},66640,14,{"v":3450384.4,"d":"3450384"},{"v":835.6,"d":"836"},{"v":19.797551789077215,"d":"19.80"},{"v":74.85875706214688,"d":"74.86"},{"v":1.647834274952919,"d":"1.65"},{"v":0.03259003116951297,"d":"0.03"},{"v":2.1028742365279016,"d":"2.10"},{"v":1.894783556235777,"d":"1.89"}]
["50X","deepvariant","HG003",3471463,1077,3470005,846,1458,231,128711,772,3342750,305,65154,17,3406307,1060]
["50X","deepvariant","HG004",3506769,1030,3505341,791,1428,239,146586,735,3360181,295,65845,10,3440922,1020]
["50X","deepvariant","HG006",3448815,516,3448155,409,660,107,29533,377,3419280,139,66251,18,3382562,498]
["50X","deepvariant","HG007",3466895,569,3466267,475,628,94,30716,452,3436177,117,66544,6,3400349,563]