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["Supplementary Table 13. Total differentially methylated promoters (DMPs) in CHG context"]
["ID","chr","from","to","strand","met_WT","unmet_WT","met_PHYA","unmet_PHYA","X.met_WT","X.met_PHYA","X.diff_PHYA.ctrl","FDR_diff_PHYA.WT","logFC_PHYA","logCPM_PHYA","PValue_PHYA","padj_PHYA"]
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["Solyc00g005283","SL3.0ch00",2354618,2356618,"-",765,182,666,236,80.781,73.836,-6.9454948173366,0.00176686621377686,3.15586622462973,-3.22628728327423,0.109234581913757,1]
["Solyc00g005430","SL3.0ch00",2358571,2360571,"-",624,232,377,225,72.897,62.625,-10.272611544074,0.000233675438158022,4.45167054452312,-3.65100820910541,0.269914950712239,1]
["Solyc00g005450","SL3.0ch00",2464349,2466349,"+",583,226,687,359,72.064,65.679,-6.3855005944123,0.011454415828611,0,-3.91085760741443,1,1]
["Solyc00g006500","SL3.0ch00",4371312,4373312,"-",20,0,11,9,100,55,-45,0.00482657205909385,0,-3.91085760741443,1,1]
["Solyc00g006520","SL3.0ch00",4370980,4372980,"+",20,0,11,9,100,55,-45,0.00482657205909385,0,-3.91085760741443,1,1]
["Solyc00g006680","SL3.0ch00",5629656,5631656,"+",13652,2749,3891,1034,83.239,79.005,-4.2337507586667,4.2964112973523e-10,0.0840124766774129,-3.31507523247684,1,1]
["Solyc00g007970","SL3.0ch00",6941525,6943525,"-",115,4,232,40,96.639,85.294,-11.344537815126,3.22072097844011E-3,0,-3.91085760741443,1,1]
["Solyc00g008580","SL3.0ch00",7582182,7584182,"+",143697,30050,38402,8683,82.705,81.559,-1.1458544765802,1.14227215507916e-07,1.77257994911729,5.85972231049318,0.00670889642388106,0.379689568495851]
["Solyc00g009090","SL3.0ch00",7841622,7843622,"-",248,590,174,668,29.594,20.665,-8.9291889409804,0.000201549067811403,1.9453065129224,-3.59635664645328,0.614062249190495,1]
["Solyc00g011150","SL3.0ch00",9131088,9133088,"-",79007,14824,22228,5090,84.201,81.368,-2.8337868815804,3.34403156164097e-26,1.56956395903939,4.09570081690159,0.0072646552041642,0.402232488146354]
["Solyc00g011160","SL3.0ch00",9129189,9131189,"+",268110,20319,66784,5268,92.955,92.689,-0.26667157725073,0.0334827543591503,1.75311895576882,5.13575323511232,3.52554005838761E-3,0.253725385932411]
["Solyc00g012430","SL3.0ch00",9551103,9553103,"+",97189,10458,24842,3625,90.285,87.266,-3.0189556508938,1.14873622122335e-45,2.22073067721275,0.15022702524476,0.0387279479336795,0.912389810082781]
["Solyc00g068970","SL3.0ch00",13555018,13557018,"-",3431,358,1423,213,90.552,86.98,-3.5711566295692,0.000631814933027684,1.52842026991486,4.99671965056755,0.0102498719122669,0.483968351670873]
["Solyc00g068980","SL3.0ch00",13553285,13555285,"+",67662,12656,20259,4404,84.243,82.143,-2.0993439534243,2.94092568736495e-13,1.97807729518833,2.42877767015063,0.00689964955537237,0.388640417789856]
["Solyc00g071180","SL3.0ch00",13651920,13653920,"-",811,523,554,452,60.795,55.07,-5.7250201936805,0.017674358313736,0,-0.604256039558963,1,1]
["Solyc00g090860","SL3.0ch00",14446495,14448495,"-",460,246,411,305,65.156,57.402,-7.7535727285676,0.00951929426755979,0,-3.91085760741443,1,1]
["Solyc00g094520","SL3.0ch00",14585676,14587676,"-",568,24580,287,18290,2.259,1.545,-0.71370777776957,1.00814123765529E-6,1.80124331289941,-2.96074051384601,1,1]
["Solyc00g094530","SL3.0ch00",14586705,14588705,"-",609,26027,324,19134,2.286,1.665,-0.62125445187034,2.3088534730906e-05,3.54249628733424,-2.86231287498452,0.334098577915024,1]
["Solyc00g099580","SL3.0ch00",14780831,14782831,"-",1404,472,1015,520,74.84,66.124,-8.7163067862178,3.95616457007626E-7,0.858324885786519,-3.48102496397314,0.809077678637095,1]
["Solyc00g110870","SL3.0ch00",15184121,15186121,"-",953,290,264,133,76.669,66.499,-10.170607796608,0.000448373371965479,-0.891235028604377,-0.0775620395219219,0.442094804413917,1]
["Solyc00g121230","SL3.0ch00",15526756,15528756,"-",166,389,139,480,29.91,22.456,-7.4543364042556,0.0132076869041325,0,-3.91085760741443,1,1]
["Solyc00g125980","SL3.0ch00",15682094,15684094,"+",447,8417,229,5570,5.043,3.949,-1.0939133194258,0.0070178446996624,0,-3.91085760741443,1,1]
["Solyc00g125990","SL3.0ch00",15682094,15684094,"+",447,8417,229,5570,5.043,3.949,-1.0939133194258,0.0070178446996624,-0.411468446647721,-0.333440414084136,0.679085781482773,1]
["Solyc00g134620","SL3.0ch00",15963948,15965948,"-",779,201,659,259,79.49,71.786,-7.7033035436397,0.000626433482628949,-2.96613334009433,-3.52840074642411,0.344241345322782,1]
["Solyc00g183050","SL3.0ch00",17411773,17413773,"+",213,178,146,179,54.476,44.923,-9.5526264017313,0.0336843629558514,0.479640175686353,-2.0440640677512,0.745093709435607,1]
["Solyc00g217960","SL3.0ch00",18350138,18352138,"+",499,261,248,175,65.658,58.629,-7.0290531292771,0.0410714031630839,-0.410296037017906,4.61513213725202,0.28525346369091,1]
["Solyc00g277510","SL3.0ch00",19798998,19800998,"-",395,36,317,61,91.647,83.862,-7.7848979241091,0.00316564408289271,0.902746187829228,0.867777264740614,0.459185748686563,1]
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["Solyc00g318130","SL3.0ch00",20685614,20687614,"+",824,49,789,74,94.387,91.425,-2.9619099574064,0.0449533527173671,1.90137383868706,-3.87171044088613,1,1]
["Solyc01g005100","SL3.0ch01",97452,99452,"-",194,429,140,451,31.14,23.689,-7.450983587412,0.012411677141088,0.168557973365495,4.06151028979403,0.632906162769226,1]
["Solyc01g005130","SL3.0ch01",122769,124769,"+",36,415,7,347,7.982,1.977,-6.0048605108547,0.000631745130867727,-0.106701452437268,4.23302293433656,0.77532486484703,1]
["Solyc01g005190","SL3.0ch01",149494,151494,"+",8,43,0,94,15.686,0,-15.686274509804,0.000858111675486964,-0.154147984764496,-1.30319441572507,0.935445539760569,1]
["Solyc01g005200","SL3.0ch01",152262,154262,"+",36,215,9,141,14.343,6,-8.3426294820717,0.034120942483682803,-2.26615490008546,-3.05078565113966,0.260618643140083,1]
["Solyc01g005210","SL3.0ch01",163331,165331,"+",196,591,125,534,24.905,18.968,-5.9365678620527,0.0215993193185713,-0.396711765398436,6.30085956494348,0.320441658192779,1]
["Solyc01g005295","SL3.0ch01",211044,213044,"-",1094,427,841,450,71.926,65.143,-6.7830644664345,0.00067930064484103,-2.4289517738633,1.99562223291417,0.00572462421677924,0.345292342303136]
["Solyc01g005380","SL3.0ch01",259020,261020,"+",70,578,30,443,10.802,6.342,-4.4599744212147,0.0284835659701442,1.03402162669027,-1.76594930308552,0.377986574586699,1]
["Solyc01g005385","SL3.0ch01",259135,261135,"+",70,608,31,456,10.324,6.366,-3.9589806957291,0.0465801455579957,0,-3.79823463900389,1,1]
["Solyc01g005510","SL3.0ch01",348880,350880,"-",341,166,237,255,67.258,48.171,-19.087650935681,1.7682542859057E-8,4.40190337836824,-3.29228058508978,0.19943629482241,1]
["Solyc01g005630","SL3.0ch01",442810,444810,"+",1116,376,943,417,74.799,69.338,-5.4606923198234,0.00495098293841157,0,-3.91085760741443,1,1]
["Solyc01g005770","SL3.0ch01",502223,504223,"-",12,33,2,51,26.667,3.774,-22.893081761006,0.00896075355270743,0,-3.65929041518187,1,1]
["Solyc01g005810","SL3.0ch01",528366,530366,"+",321,263,256,286,54.966,47.232,-7.7332810999343,0.0277086494698503,0.508555323561272,6.59136714303764,0.0726017200732907,1]
["Solyc01g005910","SL3.0ch01",588593,590593,"+",641,280,529,324,69.598,62.016,-7.5818500966761,3.32183205102672E-3,-0.0735645714428851,4.94695806981174,0.793024746832302,1]
["Solyc01g005920","SL3.0ch01",602186,604186,"-",642,650,489,657,49.69,42.67,-7.0202454087174,2.44807591689573E-3,-1.35340136927776,1.4628289871067,0.0220738410357562,0.701810796592824]
["Solyc01g005940","SL3.0ch01",612494,614494,"+",1271,479,846,571,72.629,59.704,-12.924972275431,6.24645423341773e-13,3.59439139945612,-3.56140207071382,0.382399748174349,1]
["Solyc01g005960","SL3.0ch01",623152,625152,"+",269,1046,120,647,20.456,15.645,-4.8109021866836,0.0208948840470476,-0.00414020931402563,5.87646190860859,0.988404681675053,1]
["Solyc01g005970","SL3.0ch01",640038,642038,"+",295,812,211,841,26.649,20.057,-6.5915655987992,0.00150967018290591,0.179812806282748,2.72944048577667,0.654337564663589,1]
["Solyc01g006090","SL3.0ch01",751736,753736,"+",718,168,576,222,81.038,72.18,-8.8579235900134,1.29158332805182E-4,1.0043937383064,2.58471400723856,0.0744230812291937,1]
["Solyc01g006170","SL3.0ch01",811277,813277,"-",535,130,404,214,80.451,65.372,-15.078959534759,2.00007542472426E-8,0.72746335620167,4.24441802413464,0.0673227156503958,1]
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["Solyc01g006480","SL3.0ch01",1071745,1073745,"+",1198,451,928,478,72.65,66.003,-6.6472460140074,0.000464731597922859,0.103792195258095,3.81590478711096,0.747753313849326,1]
["Solyc01g006530","SL3.0ch01",1102222,1104222,"+",1137,471,911,564,70.709,61.763,-8.9462433594738,1.87654750159523E-6,0,-3.87049148702182,1,1]
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["Solyc01g006820","SL3.0ch01",1391134,1393134,"-",24,178,14,268,11.881,4.965,-6.9166491117197,0.0181620747692523,0.293821260084062,0.0936743350930991,0.725737878669231,1]
["Solyc01g006860","SL3.0ch01",1427968,1429968,"-",1011,576,806,568,63.705,58.661,-5.0442597193904,0.0157198731275827,-0.455279551761015,1.38606228388789,0.514541415899258,1]
["Solyc01g006900","SL3.0ch01",1477626,1479626,"-",588,321,533,372,64.686,58.895,-5.7914410225553,0.031234010830968,0.33543911897511,8.42115481497965,0.296161813647753,1]
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["Solyc01g007100","SL3.0ch01",1657440,1659440,"-",841,451,663,484,65.093,57.803,-7.2899150023888,0.00122484507316054,-1.37236970696919,3.82582213566584,0.00049907741823746,0.0628556376602728]
["Solyc01g007180","SL3.0ch01",1744700,1746700,"-",1007,423,952,486,70.42,66.203,-4.2165206142953,0.0393154637131889,0.313106605592699,2.91454240468264,0.444961055716041,1]
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["Solyc01g007990","SL3.0ch01",2102280,2104280,"+",634,345,499,389,64.76,56.194,-8.5662654482879,0.000935104053666158,0.432720863149947,3.79441312794229,0.344574420421081,1]
["Solyc01g008060","SL3.0ch01",2136396,2138396,"+",1124,239,868,295,82.465,74.635,-7.8305846253617,1.80872015033063e-05,0.0153734897464689,5.47340829879028,0.954544869326723,1]
["Solyc01g008320","SL3.0ch01",2359806,2361806,"+",1835,169,1755,283,91.567,86.114,-5.4530291722737,4.62190112370066e-07,0.532497565283839,6.13020806568742,0.067043816911705,1]
["Solyc01g008430","SL3.0ch01",2451862,2453862,"-",604,272,915,526,68.95,63.498,-5.4522005583388,0.0221239945264842,0,-3.91085760741443,1,1]
["Solyc01g008440","SL3.0ch01",2455095,2457095,"+",404,329,217,307,55.116,41.412,-13.70374806036,1.78126035355246e-05,-0.162687721156035,4.55181319930701,0.670353382707562,1]
["Solyc01g008497","SL3.0ch01",2548843,2550843,"-",1127,386,797,501,74.488,61.402,-13.085615472276,3.17637275494751e-12,3.64895577037952,-0.116818044216424,0.0546759493764165,1]
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["Solyc01g008800","SL3.0ch01",2774775,2776775,"-",1011,562,686,572,64.272,54.531,-9.7410899549937,2.05338007033344E-6,0.540839507810259,-1.01086296578986,0.597212421705815,1]
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["Solyc01g008820","SL3.0ch01",2776260,2778260,"+",808,445,495,487,64.485,50.407,-14.077903459396,5.52395726290181e-10,0.382632440241939,5.72680010483188,0.177676244357175,1]
["Solyc01g008890","SL3.0ch01",2852040,2854040,"-",1318,256,1076,293,83.736,78.598,-5.1381887743026,1.7756931413036E-3,0.180061970913546,3.79301662323949,0.578853185273431,1]
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["Solyc01g009190","SL3.0ch01",3168921,3170921,"+",423,180,495,314,70.149,61.187,-8.9626035459292,0.0021707781993534,-3.92220962406137,-3.34743505505667,0.411973958815577,1]
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["Solyc12g049270","SL3.0ch12",61712421,61714421,"-",400,86,378,152,82.305,71.321,-10.98377203199,0.000272623003089602,0.5149208475824,5.9942760029849,0.0832905013236481,1]
["Solyc12g049460","SL3.0ch12",61985767,61987767,"+",1596,292,1314,309,84.534,80.961,-3.57271531063,0.0162815785980675,-2.65109578733804,-3.27443797212844,0.164788009298333,1]
["Solyc12g049500","SL3.0ch12",62089372,62091372,"-",1021,437,835,477,70.027,63.643,-6.3841421593228,1.76620019700408E-3,5.10368949681336,-3.47257437788194,0.0327652926864952,0.846172555097878]
["Solyc12g049540","SL3.0ch12",62120115,62122115,"-",516,380,331,383,57.589,46.359,-11.230742296919,6.04139084233815E-5,0.453868530978515,3.80882100971217,0.237957899276119,1]
["Solyc12g049617","SL3.0ch12",62336792,62338792,"+",618,200,601,276,75.55,68.529,-7.0210458525814,0.00541904742964755,-0.397561607224407,-1.49800398906016,0.832901538955415,1]
["Solyc12g055810","SL3.0ch12",62753343,62755343,"+",776,601,644,612,56.354,51.274,-5.0805082589771,0.0265534207806265,-0.676992451540027,1.62841615940295,0.380872367172502,1]
["Solyc12g055840","SL3.0ch12",62790185,62792185,"+",334,680,181,579,32.939,23.816,-9.1230665420949,1.94202939793639E-4,-0.609164664057514,6.27460817854397,0.12427647990372,1]
["Solyc12g055920","SL3.0ch12",62865021,62867021,"+",728,708,562,688,50.696,44.96,-5.7363788300836,0.0108543652386107,-2.64640988314236,-3.83567496299968,0.586374053639972,1]
["Solyc12g056290","SL3.0ch12",63191022,63193022,"-",39,142,4,122,21.547,3.175,-18.372358151364,1.34315231283434e-05,0.524625214492095,2.68383835324278,0.230446828335282,1]
["Solyc12g056400","SL3.0ch12",63273856,63275856,"+",779,202,532,213,79.409,71.409,-7.9993705915755,0.000749134645999924,-0.194013733040253,5.08750891650482,0.523133664602193,1]
["Solyc12g056800","SL3.0ch12",63827318,63829318,"+",421,408,310,388,50.784,44.413,-6.3714697515908,0.0344850583763769,-0.194459906137908,3.20052584841239,0.750870104356872,1]
["Solyc12g056855","SL3.0ch12",63896423,63898423,"+",1217,333,452,517,78.516,46.646,-31.870102200473,7.53474185227345e-58,1.75465672468347,-2.93856378555022,0.298190211575839,1]
["Solyc12g057040","SL3.0ch12",64057217,64059217,"+",758,401,597,448,65.401,57.129,-8.2720213350067,0.00046588308733374,-0.453011932073968,5.49977938591625,0.48735777870778,1]
["Solyc12g087930","SL3.0ch12",64417953,64419953,"+",239,360,113,270,39.9,29.504,-10.395916606006,0.00422804843678398,0,-3.91085760741443,1,1]
["Solyc12g087980","SL3.0ch12",64461958,64463958,"-",869,307,806,356,73.895,69.363,-4.5313908696008,0.0410901693069115,-1.69713785418111,0.241164295683905,0.0648573965971127,1]
["Solyc12g088080","SL3.0ch12",64546497,64548497,"+",532,783,467,832,40.456,35.951,-4.5055424324649,0.0458323629438126,0,-3.91085760741443,1,1]
["Solyc12g088190","SL3.0ch12",64610799,64612799,"+",621,641,395,772,49.208,33.847,-15.360134822245,5.2630970907964e-13,-1.68374453901512,-1.03171731523323,0.184490978800837,1]
["Solyc12g088230","SL3.0ch12",64663585,64665585,"-",1088,427,986,480,71.815,67.258,-4.5573370433906,0.0217007781877158,0.34471098078273,7.89690266693013,0.314620375260044,1]
["Solyc12g088640","SL3.0ch12",64902467,64904467,"-",431,345,304,336,55.541,47.5,-8.0412371134021,0.00951908424744846,0.59524325772445,-0.734264390814052,0.629182490427722,1]
["Solyc12g088930","SL3.0ch12",65101980,65103980,"+",429,424,280,371,50.293,43.011,-7.2823305474669,0.0172136188991055,-0.680978977277022,-1.0632047519066,0.591526651737111,1]
["Solyc12g088990","SL3.0ch12",65149909,65151909,"-",544,242,457,341,69.211,57.268,-11.943025502688,9.07038812127309e-06,-0.0462464958619355,6.0047279086467,0.86677244379321,1]
["Solyc12g089070","SL3.0ch12",65189294,65191294,"+",454,329,300,363,57.982,45.249,-12.733251272805,1.38082469331519E-5,0,-3.91085760741443,1,1]
["Solyc12g089140","SL3.0ch12",65239883,65241883,"-",259,575,191,655,31.055,22.577,-8.4783237239995,0.000527608462542079,-0.0505112198663336,8.35614918647948,0.875841836986565,1]
["Solyc12g089200","SL3.0ch12",65295608,65297608,"+",223,131,180,226,62.994,44.335,-18.659374913028,3.40800941377565e-06,0.33845580056443,-2.07141725495362,0.847761289446768,1]
["Solyc12g089220","SL3.0ch12",65312189,65314189,"-",832,373,481,366,69.046,56.789,-12.256977273952,2.10625582312658e-07,0.0718637589904409,5.78815286759122,0.86583683620014,1]
["Solyc12g089230","SL3.0ch12",65312227,65314227,"+",832,373,481,366,69.046,56.789,-12.256977273952,2.10625582312658e-07,-3.32491161732492,-1.81954448802408,0.0152544725933115,0.595657178730968]
["Solyc12g089370","SL3.0ch12",65471397,65473397,"-",210,153,171,181,57.851,48.58,-9.271694214876,0.0342886124820706,0,-3.91085760741443,1,1]
["Solyc12g094380","SL3.0ch12",65581175,65583175,"-",331,226,236,218,59.425,51.982,-7.443114861712,0.0438718436198843,0.0529010119549552,5.56764930123771,0.875938603404365,1]
["Solyc12g094400","SL3.0ch12",65599747,65601747,"+",1062,438,897,451,70.8,66.543,-4.2569732937685,0.037466367195635,0.169488776817694,-1.24059607310732,1,1]
["Solyc12g094620","SL3.0ch12",65778217,65780217,"+",450,404,402,457,52.693,46.799,-5.894605404138,0.0385908963288057,0.426299415168533,11.1837511497282,0.308678856050651,1]
["Solyc12g094640","SL3.0ch12",65790803,65792803,"+",287,302,235,418,48.727,35.988,-12.738906496593,5.47905240739271E-5,-2.68575604673778,1.00618887960525,0.00983291324754693,0.474633793573898]
["Solyc12g094700","SL3.0ch12",65824063,65826063,"+",466,820,330,742,36.236,30.784,-5.452809823356,0.0175647576428313,-5.26633179022154,-3.3919621569005,0.151170241418069,1]
["Solyc12g095760","SL3.0ch12",65878520,65880520,"-",103,208,46,180,33.119,20.354,-12.764988760208,0.0048705758290512,-0.0751353723210554,6.58628268940196,0.835278815410426,1]
["Solyc12g095850","SL3.0ch12",65942983,65944983,"+",654,244,551,264,72.829,67.607,-5.22114583191,0.0462468082614007,0.49875121328668,2.2157608933146,0.271706763022025,1]
["Solyc12g095960","SL3.0ch12",66046963,66048963,"-",1041,865,612,770,54.617,44.284,-10.333352062115,8.15291384145855e-08,0.411961261405679,8.24428412376545,0.122393596228814,1]
["Solyc12g096010","SL3.0ch12",66078212,66080212,"-",595,179,641,287,76.873,69.073,-7.8001091508509,0.00181195569321831,-0.0635405395945254,2.58814266007578,0.894810815017532,1]
["Solyc12g096070","SL3.0ch12",66124512,66126512,"+",392,151,231,146,72.192,61.273,-10.918318996048,0.00256198306578562,-0.00528736026693275,2.63665822201816,1,1]
["Solyc12g096320","SL3.0ch12",66273067,66275067,"+",609,260,408,295,70.081,58.037,-12.04356800626,7.61879124568039e-06,-0.4753556948073,0.582952288842566,0.569994742731333,1]
["Solyc12g096450","SL3.0ch12",66347984,66349984,"+",262,210,211,271,55.508,43.776,-11.732540966313,1.74178131816149E-3,0.0849078466073623,5.24549365539456,0.780668483390106,1]
["Solyc12g096670","SL3.0ch12",66485355,66487355,"-",626,782,426,691,44.46,38.138,-6.3223579799788,0.00575644636559024,0.282101787634369,6.77875002160717,0.328185515282077,1]
["Solyc12g096690","SL3.0ch12",66495101,66497101,"-",16,186,1,161,7.921,0.617,-7.3035081285906,0.00302355387622892,-0.0320582942492876,5.89978858232545,0.905566825553243,1]
["Solyc12g096710","SL3.0ch12",66497420,66499420,"+",563,189,374,203,74.867,64.818,-10.048997013164,0.000464272318956454,0.495395214862442,4.8250896844166,0.504315877560641,1]
["Solyc12g096770","SL3.0ch12",66526916,66528916,"+",187,464,147,509,28.725,22.409,-6.3165018170919,0.0255684999316599,-0.947862783027092,-1.70581697568017,0.789817791496388,1]
["Solyc12g096800","SL3.0ch12",66551524,66553524,"-",82,550,34,481,12.975,6.602,-6.372741796731,0.00174988711078596,6.43123581329105,-2.12870915060025,0.0288711253901743,0.795579670998269]
["Solyc12g096810","SL3.0ch12",66550693,66552693,"+",74,149,31,174,33.184,15.122,-18.06190528273,1.1918251696236E-4,0.216960288581112,3.81748157398507,0.55876418028193,1]
["Solyc12g096840","SL3.0ch12",66581525,66583525,"-",423,610,305,583,40.949,34.347,-6.6018462799683,0.0101061115526797,0,-3.60824010973034,1,1]
["Solyc12g098120","SL3.0ch12",66739898,66741898,"+",566,576,319,523,49.562,37.886,-11.676185880503,2.6069088763216e-06,0,-3.87342270417847,1,1]
["Solyc12g098190","SL3.0ch12",66794141,66796141,"-",1633,241,1369,260,87.14,84.039,-3.1005199908542,0.0276727652767691,0.209696052905931,4.74397987545438,0.468665243911544,1]
["Solyc12g098270","SL3.0ch12",66827590,66829590,"+",576,190,487,220,75.196,68.883,-6.3132199083392,0.0212771199203224,0,-3.91085760741443,1,1]
["Solyc12g098310","SL3.0ch12",66847837,66849837,"+",517,300,402,381,63.28,51.341,-11.939297589068,1.39481924682119E-5,0.810602279322988,3.93054776337667,0.094394316654922,1]
["Solyc12g098410","SL3.0ch12",66902750,66904750,"+",366,350,293,409,51.117,41.738,-9.3794266978624,2.03447634297495E-3,0,-3.79913482239491,1,1]
["Solyc12g098420","SL3.0ch12",66902750,66904750,"+",366,350,293,409,51.117,41.738,-9.3794266978624,2.03447634297495E-3,0.155426107301253,5.85955608553069,0.571003924681491,1]
["Solyc12g098450","SL3.0ch12",66932068,66934068,"-",373,463,323,527,44.617,38,-6.6172248803828,0.0191145721696539,-1.86136248596684,-2.53228219531303,0.443174289354008,1]
["Solyc12g098460","SL3.0ch12",66934807,66936807,"+",314,570,278,637,35.52,30.383,-5.137848329748,0.0484550721037282,0,-3.91085760741443,1,1]
["Solyc12g098580","SL3.0ch12",67025973,67027973,"-",988,648,738,625,60.391,54.145,-6.2459302523737,2.80679437744731E-3,2.29289464715013,0.179830985863639,0.0683086149589706,1]
["Solyc12g098590","SL3.0ch12",67025243,67027243,"+",852,495,716,548,63.252,56.646,-6.606100758366,0.00261408951452019,-1.92065434394205,-3.68964036006616,0.999999999999999,1]
["Solyc12g098740","SL3.0ch12",67124328,67126328,"+",46,238,21,209,16.197,9.13,-7.0667483159829,0.0431919302130121,0.384792893423704,7.91005035557334,0.182029390292554,1]
["Solyc12g098770","SL3.0ch12",67150928,67152928,"-",19,2,8,11,90.476,42.105,-48.370927318296,0.00692611102391447,0,-3.87248641899473,1,1]
["Solyc12g098757","SL3.0ch12",67156543,67158543,"+",432,393,389,534,52.364,42.145,-10.218457598739,0.000136939111664327,0,-3.32454856206586,1,1]
["Solyc12g099000","SL3.0ch12",67300163,67302163,"-",218,597,137,637,26.748,17.7,-9.0482078597359,0.000128144061401297,-0.0134076795122432,7.93485967933462,0.967806214083218,1]
["Solyc12g099070","SL3.0ch12",67331543,67333543,"+",643,284,521,297,69.364,63.692,-5.6716067552348,0.0326197143047232,2.62045389919072,-3.5715005195899,0.645551372746833,1]
["Solyc12g099130","SL3.0ch12",67374354,67376354,"+",94,544,53,538,14.734,8.968,-5.7656912199184,0.00733079560271822,6.04108138846494,-2.93925070570666,0.00200978291698274,0.174904903587928]
["Solyc12g099280","SL3.0ch12",67454495,67456495,"+",303,120,269,206,71.631,56.632,-14.99962672639,2.67727475838663e-05,0.12752344902325,3.91819229589415,0.737669881543168,1]
["Solyc12g099470","SL3.0ch12",67596659,67598659,"-",473,627,315,649,43,32.676,-10.323651452282,1.35702971947648e-05,0.194679644065528,6.04285080568767,0.468666074375936,1]
["Solyc12g099515","SL3.0ch12",67624521,67626521,"-",573,524,485,617,52.233,44.011,-8.2224744270383,0.000678164615844639,-0.218448054574169,2.37241961404225,0.64715740298913,1]
["Solyc12g099530","SL3.0ch12",67625847,67627847,"+",477,562,366,585,45.91,38.486,-7.4237239762815,0.00377010717457107,0.179348215771916,4.55514266895669,0.538792625120151,1]
["Solyc12g099720","SL3.0ch12",67724258,67726258,"+",67,460,11,531,12.713,2.03,-10.683952190566,1.12692932011351E-10,-0.973034292373928,-3.79760289006955,1,1]
["Solyc12g099900","SL3.0ch12",67825277,67827277,"+",141,927,83,1064,13.202,7.236,-5.9659786644201,3.33794395683815e-05,0.772098457614761,4.02006486106073,0.102581100032449,1]
["Solyc12g100100","SL3.0ch12",67934890,67936890,"+",552,407,442,483,57.56,47.784,-9.7761745061015,0.000151276235216738,0,-3.91085760741443,1,1]
["Solyc12g100110","SL3.0ch12",67937489,67939489,"+",1037,449,644,478,69.785,57.398,-12.387152340442,1.59925014022766E-9,2.54569711327284,-3.48659240768133,0.626546065817986,1]

{"sheet":"PHYA_vs_WT_IG_hypermethylated","index":1,"n_rows":7581,"n_cols":17,"rows_kept":4500,"cut":true,"bounds":{"rows_first":2000,"rows_last":500,"rows_between":2000,"halvings":0}}
["Supplementary Table 13. Total differentially methylated promoters (DMPs) in CHG context"]
["ID","chr","from","to","strand","met_WT","unmet_WT","met_PHYA","unmet_PHYA","X.met_WT","X.met_PHYA","X.diff_PHYA.ctrl","FDR_diff_PHYA.WT","logFC_PHYA","logCPM_PHYA","PValue_PHYA","padj_PHYA"]
["Solyc00g005060","SL3.0ch00",724013,726013,"-",121,22,168,4,84.615,97.674,13.059033989266,2.61498176251716E-4,0,-3.91085760741443,1,1]
["Solyc00g005084","SL3.0ch00",807592,809592,"+",873,230,718,125,79.148,85.172,6.024225959827,3.0960811706337E-3,0,-3.91085760741443,1,1]
["Solyc00g005092","SL3.0ch00",1125793,1127793,"+",351,191,267,103,64.76,72.162,7.4020145606861,0.0482658815242077,0.611398718852829,-1.17335822979058,0.607017724938602,1]
["Solyc00g005096","SL3.0ch00",1732561,1734561,"+",877,346,851,248,71.709,77.434,5.7251184269949,0.00620395316138747,0,-3.91085760741443,1,1]
["Solyc00g005460","SL3.0ch00",2490753,2492753,"-",785,199,879,167,79.776,84.034,4.2579940617762,0.0334058285793485,0,-3.91085760741443,1,1]
["Solyc00g006020","SL3.0ch00",3943107,3945107,"+",999,110,674,35,90.081,95.063,4.9823154826328,0.000674474286260566,0,-3.91085760741443,1,1]
["Solyc00g005903","SL3.0ch00",4162096,4164096,"+",3247,936,3959,961,77.624,80.467,2.843764637742,0.00378751256068717,0,-3.91085760741443,1,1]
["Solyc00g005907","SL3.0ch00",4172134,4174134,"+",4214,1324,4949,1266,76.092,79.63,3.5374754457392,3.60511998713549e-05,0,-3.91085760741443,1,1]
["Solyc00g006510","SL3.0ch00",4370359,4372359,"+",50,33,72,21,60.241,77.419,17.178390983288,0.0369579162638059,0,-3.91085760741443,1,1]
["Solyc00g006650","SL3.0ch00",5617777,5619777,"-",423,205,695,167,67.357,80.626,13.26976221792,1.08346818111015E-7,0,-3.91085760741443,1,1]
["Solyc00g006655","SL3.0ch00",5619735,5621735,"-",373,134,575,142,73.57,80.195,6.6252382956599,0.0197985826397225,0,-3.91085760741443,1,1]
["Solyc00g006660","SL3.0ch00",5628502,5630502,"+",168,83,385,107,66.932,78.252,11.319761603991,0.00405694433232309,0,-3.91085760741443,1,1]
["Solyc00g006805","SL3.0ch00",5780749,5782749,"-",1284,207,862,94,86.117,90.167,4.0506638155292,0.0101426916144984,2.23225581121544,-2.36691828856068,0.170800710893164,1]
["Solyc00g006867","SL3.0ch00",6390079,6392079,"+",35,859,438,275,3.915,61.431,57.515586220745,4.27462510758986e-151,-0.716583498540333,-0.558251759538668,0.439300483574759,1]
["Solyc00g007550","SL3.0ch00",6650039,6652039,"-",285,354,310,253,44.601,55.062,10.461227995564,0.00162764288567153,-4.21040546350359,-3.43052628147651,0.183523757110152,1]
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["Solyc12g094660","SL3.0ch12",65804016,65806016,"-",125,269,132,191,31.726,40.867,9.1409847401424,0.0318468006673666,-0.24105567673772,2.42754636493707,0.760347387225659,1]
["Solyc12g094690","SL3.0ch12",65820137,65822137,"+",895,364,792,241,71.088,76.67,5.5817283035523,0.00931282248505453,0.35300200461012,-1.49909869154264,0.768084868953016,1]
["Solyc12g094710","SL3.0ch12",65834878,65836878,"-",766,989,699,706,43.647,49.751,6.1041660329917,0.00284784012130591,-0.0116837449644198,5.45358432769675,0.967402579227492,1]
["Solyc12g094720","SL3.0ch12",65834448,65836448,"+",755,1259,690,936,37.488,42.435,4.9478374624859,0.0093621034593582,-1.7628983235746,1.54992103460389,0.0970382970085229,1]
["Solyc12g095920","SL3.0ch12",66004479,66006479,"-",340,883,300,532,27.8,36.058,8.2572017107994,0.000490656121287526,0.330479380206533,4.981318384087,0.272728650608819,1]
["Solyc12g095940","SL3.0ch12",66009043,66011043,"+",152,327,137,148,31.733,48.07,16.337398820642,5.95799168095106E-5,0.300320470491059,3.9064735387154,0.357532454071177,1]
["Solyc12g095950","SL3.0ch12",66038500,66040500,"+",548,436,453,194,55.691,70.015,14.324399039972,8.26470356582383e-08,0,-3.91085760741443,1,1]
["Solyc12g095970","SL3.0ch12",66051031,66053031,"-",319,1116,284,788,22.23,26.493,4.2625721566384,0.0354412266986556,-3.28403146616092,-3.79436498907682,0.5290256631869,1]
["Solyc12g095980","SL3.0ch12",66052081,66054081,"+",598,1182,595,828,33.596,41.813,8.217565358832,1.84283085958681e-05,-0.938450271284396,2.35919685876181,0.202530048012485,1]
["Solyc12g096000","SL3.0ch12",66069725,66071725,"-",775,521,829,345,59.799,70.613,10.81390518855,2.58109289879045e-07,0.210716813522823,8.34712113923145,0.416206444026816,1]
["Solyc12g096040","SL3.0ch12",66100925,66102925,"-",196,645,224,484,23.306,31.638,8.3328294940782,1.46296666155485E-3,0.0996318471243616,4.19756871392804,0.742300223986675,1]
["Solyc12g096080","SL3.0ch12",66134014,66136014,"-",284,666,242,389,29.895,38.352,8.4570856618567,0.00261971346590376,-0.767415658577224,-0.452546272656871,0.549446873778933,1]
["Solyc12g096120","SL3.0ch12",66155101,66157101,"-",569,275,653,242,67.417,72.961,5.5438322433742,0.0308931974465063,0.129760100085069,5.73272113932236,0.727847032570644,1]
["Solyc12g096130","SL3.0ch12",66155466,66157466,"+",398,379,449,263,51.223,63.062,11.839146530158,3.38067245645641e-05,1.46211676688129,0.0059994057314241,0.0934485584393846,1]
["Solyc12g096140","SL3.0ch12",66163437,66165437,"-",208,544,277,471,27.66,37.032,9.3725110934122,0.000624205849213207,0.217361883582275,4.45420081886258,0.473412563201141,1]
["Solyc12g096150","SL3.0ch12",66162179,66164179,"+",207,504,274,298,29.114,47.902,18.788173851465,1.4441883388534e-10,0.198212785642255,7.31954264768649,0.572313613134213,1]
["Solyc12g096240","SL3.0ch12",66232042,66234042,"+",295,355,365,308,45.385,54.235,8.8501543033489,0.00544320461140224,0,-3.91085760741443,1,1]
["Solyc12g096300","SL3.0ch12",66264178,66266178,"-",351,196,430,132,64.168,76.512,12.344265388043,5.77653151291601e-05,0.355807635506991,8.2716479712872,0.215284887014281,1]
["Solyc12g096340","SL3.0ch12",66280695,66282695,"+",1596,863,1492,614,64.904,70.845,5.9407714823196,0.000146348918871922,0.277074707910322,6.87808856816368,0.356651989357124,1]
["Solyc12g096370","SL3.0ch12",66302913,66304913,"-",794,540,787,347,59.52,69.4,9.8801128536261,3.67317133972855e-06,0.135667649871751,3.6558873266412,0.695487474792553,1]
["Solyc12g096380","SL3.0ch12",66306721,66308721,"-",413,836,394,421,33.066,48.344,15.277105119679,1.25258919467879e-10,0,-3.91085760741443,1,1]
["Solyc12g096390","SL3.0ch12",66305710,66307710,"+",428,532,516,509,44.583,50.341,5.7581300813008,0.0279390208209015,0.116035152165693,4.22991938580522,0.751728653038957,1]
["Solyc12g096420","SL3.0ch12",66322073,66324073,"+",80,170,110,146,32,42.969,10.96875,0.0335366046448924,0.726269763381613,5.8012567921597,0.0303464770953015,0.81335858510671]
["Solyc12g096430","SL3.0ch12",66344617,66346617,"-",1131,266,970,140,80.959,87.387,6.4281891053545,1.11811425104642E-4,-1.45598576609876,-0.111257441783025,0.0355262811577911,0.87937994771756]
["Solyc12g096635","SL3.0ch12",66445925,66447925,"+",212,1005,170,554,17.42,23.481,6.0607780204016,0.00542827291278272,0,-3.91085760741443,1,1]
["Solyc12g096720","SL3.0ch12",66501687,66503687,"+",29,283,90,261,9.295,25.641,16.346153846154,3.86699588368063E-7,-0.409013880848623,0.120216265603784,0.913014485080676,1]
["Solyc12g096820","SL3.0ch12",66564631,66566631,"+",553,391,604,316,58.581,65.652,7.0716654384672,0.00697168494700464,-0.884816358435803,2.58513192743009,0.0372220617377758,0.897393805611632]
["Solyc12g096850","SL3.0ch12",66592796,66594796,"-",829,414,929,361,66.693,72.016,5.3220203683262,0.0125145003574532,2.70294798957334,-3.79683296932688,0.655579132476715,1]
["Solyc12g096860","SL3.0ch12",66593955,66595955,"+",993,550,1082,470,64.355,69.716,5.3613425446479,0.0063366767563814,0.0770935548323717,2.37586255887294,0.938720966846293,1]
["Solyc12g096910","SL3.0ch12",66617457,66619457,"-",478,1376,468,886,25.782,34.564,8.7821612896544,1.11974752817381E-6,0,-3.22930841105345,1,1]
["Solyc12g096920","SL3.0ch12",66620584,66622584,"+",177,694,183,492,20.321,27.111,6.7896415359102,0.00713757418666938,-0.622020761970284,-0.617263860023718,0.586335750585372,1]
["Solyc12g096980","SL3.0ch12",66651308,66653308,"+",566,352,560,173,61.656,76.398,14.742589471744,2.88085122769133e-09,-0.768780138657781,-2.64171832312473,0.786088672674825,1]
["Solyc12g097050","SL3.0ch12",66681844,66683844,"+",175,213,210,98,45.103,68.182,23.078725398313,1.93620207284633e-08,3.82587813326525,-3.19895789505985,0.205887531534474,1]
["Solyc12g098100","SL3.0ch12",66729036,66731036,"+",406,310,438,238,56.704,64.793,8.0889887937589,0.00762097157983178,-1.13767849493389,-3.60253566581618,0.795122463652444,1]
["Solyc12g098180","SL3.0ch12",66787244,66789244,"+",384,176,472,54,68.571,89.734,21.162411732754,1.5004794208853E-16,2.16290975582041,-1.11831569942161,0.220533844271596,1]
["Solyc12g098250","SL3.0ch12",66826054,66828054,"-",691,625,785,394,52.508,66.582,14.074250240403,2.2339675901109e-11,0,-3.91085760741443,1,1]
["Solyc12g098330","SL3.0ch12",66857687,66859687,"+",259,239,296,174,52.008,62.979,10.970691275741,0.00256991983644726,0.235527336928045,6.82266978338076,0.469606040353099,1]
["Solyc12g098480","SL3.0ch12",66959918,66961918,"-",505,690,551,619,42.259,47.094,4.8346028680757,0.0437044718603453,-1.13533114475625,-3.76700870201958,0.79954920214593,1]
["Solyc12g098510","SL3.0ch12",66975596,66977596,"-",610,411,689,282,59.745,70.958,11.212427790851,1.908909858552E-6,-0.373165627167695,3.37595498466805,0.34764691260332,1]
["Solyc12g098530","SL3.0ch12",66989051,66991051,"-",1318,132,1222,83,90.897,93.64,2.7432950191571,0.0234193211249585,0.323997109138731,4.03379373495084,0.303602580486851,1]
["Solyc12g098560","SL3.0ch12",67012789,67014789,"-",534,374,592,326,58.811,64.488,5.6774447419692,0.0354365999547528,0,-3.91085760741443,1,1]
["Solyc12g098670","SL3.0ch12",67075727,67077727,"+",361,467,382,336,43.599,53.203,9.6043088019593,1.01165258567563E-3,-0.109973928414454,4.31489245306894,0.789581660829645,1]
["Solyc12g098680","SL3.0ch12",67084610,67086610,"+",188,642,203,446,22.651,31.279,8.6282881912859,0.00115917423882006,0.846186795654068,-3.49594036003781,0.784144282467019,1]
["Solyc12g098750","SL3.0ch12",67138754,67140754,"-",107,447,125,364,19.314,25.562,6.2482927657564,0.0410389184986825,0,-3.91085760741443,1,1]
["Solyc12g098920","SL3.0ch12",67263883,67265883,"-",666,195,720,109,77.352,86.852,9.4997120917271,3.8486615920935e-06,-0.0741547200339513,4.23972610830657,0.846873491944468,1]
["Solyc12g099090","SL3.0ch12",67340163,67342163,"+",114,513,110,232,18.182,32.164,13.98192450824,1.37325495134707E-5,0.259743952670285,5.55210792992616,0.356805621542336,1]
["Solyc12g099140","SL3.0ch12",67381709,67383709,"+",143,538,195,504,20.999,27.897,6.8984641369357,0.010804198172352,4.47672603536105e-05,1.99885098853957,1,1]
["Solyc12g099150","SL3.0ch12",67388430,67390430,"-",1281,540,1212,345,70.346,77.842,7.4960400973866,7.37686449827208e-06,-1.80441672421593,-3.87399169536477,0.999999999999999,1]
["Solyc12g099170","SL3.0ch12",67396065,67398065,"+",408,471,439,380,46.416,53.602,7.1855713493939,0.0116681124907916,-0.308764705656795,2.43600541217631,0.538657891659612,1]
["Solyc12g099175","SL3.0ch12",67397335,67399335,"+",271,461,343,316,37.022,52.049,15.026700498354,2.48061295436332e-07,-0.527209679808168,2.62439032715876,0.233037149516778,1]
["Solyc12g099220","SL3.0ch12",67421279,67423279,"-",764,548,860,498,58.232,63.328,5.0967168360933,0.020328026375405,0,-3.91085760741443,1,1]
["Solyc12g099270","SL3.0ch12",67455648,67457648,"-",315,573,275,296,35.473,48.161,12.688147867658,1.72690614100415e-05,-0.161370807643022,6.00857272405455,0.633001266435113,1]
["Solyc12g099290","SL3.0ch12",67474851,67476851,"-",340,364,315,239,48.295,56.859,8.5637512307187,0.009069007308202,-0.726839415795278,2.95743426434154,0.0895571349173809,1]
["Solyc12g099300","SL3.0ch12",67474325,67476325,"+",339,758,318,397,30.902,44.476,13.573063217548,9.21756092644987e-08,-1.62029159439233,-3.42511387267245,0.628892290603587,1]
["Solyc12g099330","SL3.0ch12",67503363,67505363,"-",230,602,305,610,27.644,33.333,5.6891025641026,0.0289218193542553,0.797205973872041,6.74897606902199,0.0224328055238896,0.704925469528395]
["Solyc12g099460","SL3.0ch12",67587479,67589479,"-",133,644,128,440,17.117,22.535,5.4180941504885,0.0363507811855462,0,-3.91085760741443,1,1]
["Solyc12g099490","SL3.0ch12",67600934,67602934,"+",787,357,724,249,68.794,74.409,5.6153378995106,0.0140353778007785,0.0669862860757885,6.299373887455,0.819935035276217,1]
["Solyc12g099500","SL3.0ch12",67608122,67610122,"-",186,713,191,498,20.69,27.721,7.0316800960913,0.00505159738144654,0.314840396648613,7.35397338436693,0.421040423550303,1]
["Solyc12g099540","SL3.0ch12",67641984,67643984,"-",215,136,191,66,61.254,74.319,13.065504894299,3.74034016334786E-3,0.486040594270421,0.246625329534406,0.622926030643148,1]
["Solyc12g099580","SL3.0ch12",67662948,67664948,"+",511,447,529,246,53.34,68.258,14.917772240555,4.79388481265372e-09,-1.25664371705824,-0.341522734793326,0.249120800137879,1]
["Solyc12g099710","SL3.0ch12",67720254,67722254,"+",18,366,44,74,4.688,37.288,32.60063559322,4.45699045381364e-16,-0.150755330513768,5.2151773837404,0.631229279611536,1]
["Solyc12g099740","SL3.0ch12",67751571,67753571,"-",493,566,478,426,46.553,52.876,6.3227539756157,0.0172541175701228,0.404014816358874,4.85580092332481,0.252497222615823,1]
["Solyc12g099760","SL3.0ch12",67759715,67761715,"-",9,452,39,450,1.952,7.975,6.0231824654326,1.39239382739438E-4,0.471200361621848,5.85725792045328,0.135996209704533,1]
["Solyc12g099790","SL3.0ch12",67767903,67769903,"+",127,244,177,199,34.232,47.074,12.842662155187,0.00210094113322844,0.316419213280958,0.767000589637595,0.673173771496701,1]
["Solyc12g099800","SL3.0ch12",67779125,67781125,"-",26,952,50,672,2.658,6.925,4.2667210486662,0.000259758912383592,-0.448662970287984,4.92019589445467,0.17355085747043,1]
["Solyc12g099850","SL3.0ch12",67807817,67809817,"-",44,241,43,13,15.439,76.786,61.347117794486,1.62841629500941e-17,0,-3.91085760741443,1,1]
["Solyc12g099910","SL3.0ch12",67830642,67832642,"+",1595,148,1496,89,91.509,94.385,2.8759653304521,0.00560369251607223,0.180225491656214,6.38411987643982,0.536246818629284,1]
["Solyc12g100035","SL3.0ch12",67914214,67916214,"-",868,710,771,514,55.006,60,4.9936628643853,0.0222029002361841,0,-3.91085760741443,1,1]
["Solyc12g100150","SL3.0ch12",67963908,67965908,"+",71,291,58,142,19.613,29,9.3867403314917,0.0316188299495621,3.20171349412838,-2.47412922827029,0.121878332286905,1]
["Solyc12g100180","SL3.0ch12",67977198,67979198,"+",145,623,159,502,18.88,24.054,5.1742546016137,0.0458319975732268,-4.62267484549214,-3.48457333746722,0.156372752824372,1]
["Solyc12g100220","SL3.0ch12",68000736,68002736,"+",2,81,15,25,2.41,37.5,35.090361445783,4.91131710484507e-06,0,-3.57601201221185,1,1]
["Solyc12g100340","SL3.0ch12",68086246,68088246,"-",833,176,702,103,82.557,87.205,4.647981828143,0.0206392349663883,0,-3.91085760741443,1,1]
["Solyc12g100353","SL3.0ch12",68098699,68100699,"+",9,783,29,801,1.136,3.494,2.3576122672508,0.00610491046277714,0,-3.91085760741443,1,1]

{"sheet":"PHYA_vs_WT_BK_hypomethylated","index":2,"n_rows":4682,"n_cols":17,"rows_kept":4682}
["Supplementary Table 13. Total differentially methylated promoters (DMPs) in CHG context"]
["ID","chr","from","to","strand","met_WT","unmet_WT","met_PHYA","unmet_PHYA","X.met_WT","X.met_PHYA","X.diff_PHYA.ctrl","FDR_diff_PHYA.WT","logFC_PHYA","logCPM_PHYA","PValue_PHYA","padj_PHYA"]
["Solyc00g005050","SL3.0ch00",575385,577385,"-",839,111,689,219,88.316,75.881,-12.434732204962,6.36083053677084e-11,0.128812259749881,6.25879772751795,0.625383670868696,1]
["Solyc00g005450","SL3.0ch00",2464349,2466349,"+",628,161,372,207,79.594,64.249,-15.345718657447,9.10596698869826e-09,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g005840","SL3.0ch00",3431254,3433254,"-",609,116,610,163,84,78.913,-5.0866752910737,0.0342805062008236,1.04419105664009,3.84266514413295,0.0144072627014657,0.166931963817954]
["Solyc00g006510","SL3.0ch00",4370359,4372359,"+",63,2,52,36,96.923,59.091,-37.832167832168,2.21019363092149E-7,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g006680","SL3.0ch00",5629656,5631656,"+",9978,1725,2989,679,85.26,81.489,-3.7716400766294,1.10206866123513e-06,-0.137645912798229,-3.31507523247684,1,1]
["Solyc00g006820","SL3.0ch00",5819900,5821900,"+",855,615,695,657,58.163,51.405,-6.7579398623355,1.86879466156879E-3,-1.12822449605065,1.61308375064248,0.333196526132593,1]
["Solyc00g007555","SL3.0ch00",6673303,6675303,"+",586,63,647,130,90.293,83.269,-7.023774820385,0.000874595859768217,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g008140","SL3.0ch00",7121907,7123907,"-",178,23,139,37,88.557,78.977,-9.5799412030755,0.0436964279247142,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g008580","SL3.0ch00",7582182,7584182,"+",87235,14590,42352,7924,85.671,84.239,-1.4324944963268,6.32515823878273e-12,0.871766617432193,5.85972231049318,0.173186032593562,0.748401354815333]
["Solyc00g010530","SL3.0ch00",8854847,8856847,"-",18824,3075,11510,2077,85.958,84.713,-1.2449340170331,0.00577767674350872,0.733784406619953,-2.83968867727814,0.570789085383024,1]
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["Solyc12g099420","SL3.0ch12",67550697,67552697,"+",32,182,0,71,14.953,0,-14.953271028037,7.53733560375117E-4,-0.581418301735325,3.79986932988691,0.0846341326118266,0.511869065820056]
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["Solyc12g099490","SL3.0ch12",67600934,67602934,"+",643,288,594,431,69.066,57.951,-11.114301433025,5.29523732012872e-06,0.350415335172827,6.299373887455,0.233303502559024,0.861011453933368]
["Solyc12g099520","SL3.0ch12",67627400,67629400,"-",253,195,265,298,56.473,47.069,-9.4039425272773,0.013315594987754,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g099530","SL3.0ch12",67625847,67627847,"+",257,436,173,408,37.085,29.776,-7.3088892366001,0.0208606789872398,-0.31365324293973,4.55514266895669,0.284043566592704,0.947730437489537]
["Solyc12g099600","SL3.0ch12",67668528,67670528,"+",133,291,124,393,31.368,23.985,-7.3833984161162,0.035982730569704,0.612488759963513,3.96312420906162,0.0893445124661166,0.526991181050141]
["Solyc12g099710","SL3.0ch12",67720254,67722254,"+",38,16,23,37,70.37,38.333,-32.037037037037,0.00370331931847156,0.254700922099999,5.2151773837404,0.414819584671262,1]
["Solyc12g099720","SL3.0ch12",67724258,67726258,"+",62,394,5,349,13.596,1.412,-12.184061849539,4.2571494706474e-10,-5.12548240610387e-15,-3.79760289006955,1,1]
["Solyc12g100000","SL3.0ch12",67893948,67895948,"+",24,168,6,214,12.5,2.727,-9.7727272727273,1.19711292277425E-3,-0.220465112305279,5.03909922455397,0.444875227844319,1]
["Solyc12g100110","SL3.0ch12",67937489,67939489,"+",917,453,708,463,66.934,60.461,-6.47316224825,3.90498883473284E-3,-5.12548240610387e-15,-3.48659240768133,1,1]
["Solyc12g100170","SL3.0ch12",67973773,67975773,"+",19,129,0,98,12.838,0,-12.837837837838,0.000346596854218314,6.34061938739743,-0.840707422538963,4.2680800989468E-3,0.070156566626438]
["Solyc12g100310","SL3.0ch12",68065572,68067572,"-",546,468,352,538,53.846,39.551,-14.295592048401,1.1747429403229e-08,-0.118163466870582,5.72997225902678,0.701329744044597,1]
["Solyc12g100320","SL3.0ch12",68069678,68071678,"-",62,304,45,554,16.94,7.513,-9.427369842269,0.000108919572375581,0.250006869170965,4.36975612256774,0.411901287516179,1]
["Solyc12g100330","SL3.0ch12",68068710,68070710,"+",62,304,38,358,16.94,9.596,-7.3439311144229,0.0133842537510677,-0.260654353642884,5.77562078176169,0.376857468899633,1]

{"sheet":"PHYA_vs_WT_BK_hypermethylated","index":3,"n_rows":4377,"n_cols":17,"rows_kept":4377}
["Supplementary Table 13. Total differentially methylated promoters (DMPs) in CHG context"]
["ID","chr","from","to","strand","met_WT","unmet_WT","met_PHYA","unmet_PHYA","X.met_WT","X.met_PHYA","X.diff_PHYA.ctrl","FDR_diff_PHYA.WT","logFC_PHYA","logCPM_PHYA","PValue_PHYA","padj_PHYA"]
["Solyc00g005084","SL3.0ch00",807592,809592,"+",622,151,612,102,80.466,85.714,5.248567732397,0.0268315635193048,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g005280","SL3.0ch00",2188964,2190964,"+",199,33,349,22,85.776,94.07,8.2942187935682,0.0038238124951125,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g005850","SL3.0ch00",3432603,3434603,"-",1029,187,927,116,84.622,88.878,4.2565253317859,0.0133255608842625,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g005903","SL3.0ch00",4162096,4164096,"+",2442,605,3447,726,80.144,82.602,2.4580399525573,0.0259687204297831,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g005907","SL3.0ch00",4172134,4174134,"+",2745,856,4305,940,76.229,82.078,5.8493443591164,6.73600553883787e-10,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g006867","SL3.0ch00",6390079,6392079,"+",42,550,573,293,7.095,66.166,59.071687160602,2.17090500169062e-123,-1.16640477726207,-0.558251759538668,0.264940951927419,0.916391835271242]
["Solyc00g006870","SL3.0ch00",6404880,6406880,"+",705,453,1044,472,60.881,68.865,7.9846063406565,0.000170990596261517,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g007550","SL3.0ch00",6650039,6652039,"-",240,341,318,325,41.308,49.456,8.1475870154691,0.0170634495444844,-5.12548240610387e-15,-3.43052628147651,1,1]
["Solyc00g007980","SL3.0ch00",6942523,6944523,"-",135,23,99,2,85.443,98.02,12.576764005514,0.00246104496970895,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g008020","SL3.0ch00",6991194,6993194,"-",3,9,53,6,25,89.831,64.830508474576,0.000106158556006848,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g008040","SL3.0ch00",7005181,7007181,"-",153,84,400,77,64.557,83.857,19.300480322692,2.66111890152652e-07,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g008070","SL3.0ch00",7078627,7080627,"+",58,14,169,10,80.556,94.413,13.857852265674,0.00680745532626022,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g008260","SL3.0ch00",7277831,7279831,"+",556,135,795,137,80.463,85.3,4.8373322236232,0.0317900363532322,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g008570","SL3.0ch00",7584122,7586122,"-",190538,25693,118107,13436,88.118,89.786,1.6680495486531,1.12367473675123e-49,0.733882919003458,4.3254472958713,0.197972540967892,0.798869655636904]
["Solyc00g009020","SL3.0ch00",7793998,7795998,"+",1075,302,1075,197,78.068,84.513,6.444314273578,1.9866392998301E-4,0.411952968841422,7.62400916820391,0.108978270167646,0.588988250203753]
["Solyc00g009050","SL3.0ch00",7822149,7824149,"-",1807,570,2145,445,76.02,82.819,6.7983392972875,6.4429265013282e-08,1.89759751253306,-1.83143939226503,1,1]
["Solyc00g009140","SL3.0ch00",7885380,7887380,"+",69,382,88,216,15.299,28.947,13.648033609523,9.50478300412507e-05,-0.0992773001808349,3.36058126720056,0.823748897546176,1]
["Solyc00g009142","SL3.0ch00",8038913,8040913,"+",621,199,1610,293,75.732,84.603,8.8715506965895,1.11677778393456e-06,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g009143","SL3.0ch00",8048016,8050016,"+",924,199,1285,209,82.28,86.011,3.7311013123434,0.0313035479754191,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g010930","SL3.0ch00",9019959,9021959,"+",772,210,1448,265,78.615,84.53,5.9149929317321,0.000840762874873657,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g011160","SL3.0ch00",9129189,9131189,"+",136824,11114,78196,5215,92.487,93.748,1.2604336577207,2.47956599492311e-28,0.727152138952346,5.13575323511232,0.215666822815156,0.830473266102548]
["Solyc00g011870","SL3.0ch00",9381599,9383599,"-",888,97,907,65,90.152,93.313,3.1604729376867,0.0386800756935181,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g012700","SL3.0ch00",9627415,9629415,"-",423,129,931,197,76.63,82.535,5.9050262102991,0.0166746344377735,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g012704","SL3.0ch00",9696804,9698804,"-",2525,960,3881,1280,72.453,75.199,2.7452333289874,0.0155963119903007,-2.0162764433785,-3.86688671544589,1,1]
["Solyc00g012706","SL3.0ch00",9705530,9707530,"-",760,337,1135,389,69.28,74.475,5.1952114691224,0.0131905005696949,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g013185","SL3.0ch00",9897786,9899786,"+",698,243,1326,340,74.176,79.592,5.4154286581795,0.0074278001918708,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g013188","SL3.0ch00",9963268,9965268,"+",301,90,407,78,76.982,83.918,6.9354285864951,0.0353608223052225,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g014395","SL3.0ch00",10046778,10048778,"+",994,303,1107,245,76.638,81.879,5.2403019257002,0.00447661592290044,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g016790","SL3.0ch00",10444493,10446493,"+",1583,565,2765,660,73.696,80.73,7.0334651823458,2.06496820123156e-08,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g017760","SL3.0ch00",10585381,10587381,"-",2249,692,2777,609,76.471,82.014,5.5435877836072,9.33009415037699e-07,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g020540","SL3.0ch00",10903182,10905182,"+",1071,279,1306,218,79.333,85.696,6.3622047244094,8.12691206767904e-05,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g022090","SL3.0ch00",11058576,11060576,"-",86,7400,265,15276,1.149,1.705,0.55635586359235,0.00496269166395063,-0.1614478719541,-3.7903905899943,1,1]
["Solyc00g024570","SL3.0ch00",11259566,11261566,"+",3850,959,4593,895,80.058,83.692,3.6334667990715,2.27198382094199E-5,-5.12548240610387e-15,-3.7595815468704,1,1]
["Solyc00g026165","SL3.0ch00",11408797,11410797,"+",22,16,369,81,57.895,82,24.105263157895,0.00496269166395063,-5.12548240610387e-15,-3.87282557379725,1,1]
["Solyc00g030510","SL3.0ch00",11649548,11651548,"+",168,232,247,229,42,51.891,9.890756302521,0.013281972877746,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g030520","SL3.0ch00",11657277,11659277,"-",841,191,979,161,81.492,85.877,4.3849449204406,0.0205205758725284,0.152046891263846,3.52117013121424,0.700920671451114,1]
["Solyc00g032947","SL3.0ch00",11830799,11832799,"-",23,20,73,18,53.488,80.22,26.731408126757,0.0084517752271235,1.80064905758787,-3.57533435268597,0.999999999999999,1]
["Solyc00g040390","SL3.0ch00",12201979,12203979,"+",93,160,125,136,36.759,47.893,11.133827025881,0.0359254340872126,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g047200","SL3.0ch00",12554728,12556728,"-",747,269,772,210,73.524,78.615,5.0914492358516,0.0272095612465204,0.674503210433851,-3.52199835793395,0.86777483438143,1]
["Solyc00g053440","SL3.0ch00",12855297,12857297,"+",13,880,31,926,1.456,3.239,1.7835223689184,0.0393346556957129,0.684765641295492,6.45674876136853,0.136598059955409,0.662879734204547]
["Solyc00g084650","SL3.0ch00",14212157,14214157,"-",291,72,330,42,80.165,88.71,8.5443881631565,0.00678633421293287,-2.12874495360578,-1.40438571129138,0.0746149955978699,0.479267105121523]
["Solyc00g084870","SL3.0ch00",14214156,14216156,"+",3,20,18,5,13.043,78.261,65.217391304348,1.58165267534737E-4,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc06g024210","SL3.0ch00",14392228,14394228,"-",519,145,626,117,78.163,84.253,6.0903776613858,0.0143951427651967,0.428673579856626,5.08387758340171,0.471987284015418,1]
["Solyc00g090430","SL3.0ch00",14430232,14432232,"+",2368,567,5120,495,80.681,91.184,10.502896688567,3.87887878284868e-40,1.85307933677456,-3.76012062124585,1,1]
["Solyc00g090650","SL3.0ch00",14441347,14443347,"-",306,72,479,62,80.952,88.54,7.5873602675821,0.00724730324304889,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g090660","SL3.0ch00",14441661,14443661,"-",342,76,537,75,81.818,87.745,5.9269162210339,0.0284629805711243,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g092870","SL3.0ch00",14521606,14523606,"+",2047,686,4417,907,74.899,82.964,8.0645589166332,1.20740303527231E-15,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g104940","SL3.0ch00",14969207,14971207,"-",1431,703,1750,686,67.057,71.839,4.7819108252809,0.0026766938973449,0.721209284737155,0.894012979898723,0.503200717978206,1]
["Solyc00g125275","SL3.0ch00",15678108,15680108,"-",129,34,73,5,79.141,93.59,14.448639295265,0.0161523740617748,-5.12548240610387e-15,-3.86961714799266,1,1]
["Solyc00g127670","SL3.0ch00",15736452,15738452,"-",624,865,874,788,41.907,52.587,10.679923934767,4.99097892541267e-08,-0.305148868973301,2.41383395958849,0.470278995965944,1]
["Solyc00g129980","SL3.0ch00",15812774,15814774,"-",228,54,420,54,80.851,88.608,7.7565311069216,0.0137786828631215,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g136260","SL3.0ch00",16015399,16017399,"-",36,187,101,161,16.143,38.55,22.406120562763,6.23551885367126E-7,-1.03722858244445,4.73267968873626,0.0317910087838314,0.284265761921889]
["Solyc00g139760","SL3.0ch00",16128726,16130726,"-",3694,287,5597,303,92.791,94.864,2.0736506882267,2.18994314022058E-4,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g140060","SL3.0ch00",16137850,16139850,"-",357,231,679,248,60.714,73.247,12.532747726922,5.81601531686927e-06,0.0979054031316517,3.74195134455469,0.864137833481655,1]
["Solyc00g141360","SL3.0ch00",16179624,16181624,"-",82,29,772,101,73.874,88.431,14.556824866103,0.000593385027249021,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g160785","SL3.0ch00",16794746,16796746,"-",299,63,560,67,82.597,89.314,6.7175094944795,0.0125243394638752,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc09g056230","SL3.0ch00",16856029,16858029,"+",705,156,984,162,81.882,85.864,3.9823412445044,0.0440261141163283,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g171810","SL3.0ch00",17098009,17100009,"-",25,1578,492,3315,1.56,12.924,11.363986064348,1.55518831272023e-47,1.21578855294162,1.65316464502327,0.0485788671452621,0.370857816825783]
["Solyc00g201160","SL3.0ch00",17912082,17914082,"-",255,124,305,90,67.282,77.215,9.9328679736816,0.00920847400613196,0.113118667683907,2.60889510230004,0.838115093699841,1]
["Solyc00g201165","SL3.0ch00",17919894,17921894,"-",204,48,250,21,80.952,92.251,11.298541556844,0.000996914902854679,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g212265","SL3.0ch00",18208150,18210150,"+",1270,317,1442,141,80.025,91.093,11.067656866175,2.41325492698201E-17,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g217560","SL3.0ch00",18339728,18341728,"+",64,430,500,826,12.955,37.707,24.751925061523,1.01101678060843e-24,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g217960","SL3.0ch00",18350138,18352138,"+",265,186,338,169,58.758,66.667,7.9083518107908,0.0374660115364218,1.05859388161353,4.61513213725202,0.00622284541653024,0.0912956254546569]
["Solyc00g249910","SL3.0ch00",19146953,19148953,"+",39,21,1798,165,65,91.594,26.594498217015,3.41642829652891e-07,-0.623428301371623,-3.19091904992403,0.80287785185681,1]
["Solyc00g254910","SL3.0ch00",19269195,19271195,"-",332,113,501,108,74.607,82.266,7.659268279183,0.011074474165224,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g269810","SL3.0ch00",19619201,19621201,"-",1052,233,1328,191,81.868,87.426,5.5582338370267,0.000355766064681826,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g275310","SL3.0ch00",19745967,19747967,"-",594,63,845,37,90.411,95.805,5.3940297580219,0.000297177488457698,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc03g033920","SL3.0ch00",19875093,19877093,"-",68,747,261,1589,8.344,14.108,5.7645498258995,1.97501083496841E-4,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc01g005080","SL3.0ch01",73169,75169,"-",36,291,100,334,11.009,23.041,12.032300342451,1.37963243766989E-4,-0.0265938039413134,3.48798381685626,0.961449469596671,1]
["Solyc01g005100","SL3.0ch01",97452,99452,"-",52,310,146,341,14.365,29.979,15.614825235119,1.26221925739307e-06,-0.16238493770923,4.06151028979403,0.646328604186136,1]
["Solyc01g005110","SL3.0ch01",97355,99355,"+",48,121,138,150,28.402,47.917,19.514299802761,0.000382184758844225,0.59362349068202,4.14212051470547,0.0924797459048376,0.537189080365498]
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["Solyc12g088850","SL3.0ch12",65041647,65043647,"+",186,592,279,596,23.907,31.886,7.9782592728608,2.06061637600845E-3,6.95796155370817,-2.62934790183319,0.031037652127478402,0.279003453454548]
["Solyc12g089030","SL3.0ch12",65164787,65166787,"+",499,426,622,381,53.946,62.014,8.0680121796772,2.10306835817061E-3,0.0374462197824974,5.68785219161646,0.893410756259944,1]
["Solyc12g089143","SL3.0ch12",65211820,65213820,"+",409,484,475,361,45.801,56.818,11.017509925685,5.02829075417048e-05,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g089195","SL3.0ch12",65300708,65302708,"-",259,262,326,207,49.712,61.163,11.451134886367,1.24841868683497E-3,1.19154979690792,0.561448415529223,0.084575430811984,0.511773643932168]
["Solyc12g089200","SL3.0ch12",65295608,65297608,"+",175,140,217,113,55.556,65.758,10.20202020202,0.0296962004021425,-1.76180684823867,-2.07141725495362,0.298999394712798,0.968009054019452]
["Solyc12g089320","SL3.0ch12",65431260,65433260,"-",35,105,135,110,25,55.102,30.102040816327,2.13193718468192e-07,-0.292210104382479,4.42920255048188,0.319539484246926,0.995899545363483]
["Solyc12g094410","SL3.0ch12",65609928,65611928,"+",674,555,673,441,54.841,60.413,5.5715919731562,0.021699302817691,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g094615","SL3.0ch12",65765561,65767561,"-",562,338,586,265,62.444,68.86,6.415720067894,0.017075645585272,1.40935975508849,-1.51404424966267,0.268862877753261,0.923622150034176]
["Solyc12g094645","SL3.0ch12",65794383,65796383,"+",0,48,10,26,0,27.778,27.777777777778,0.000650289015171146,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g094730","SL3.0ch12",65846343,65848343,"-",441,472,549,347,48.302,61.272,12.970021319042,5.49545212318985e-07,0.465526508948711,-0.136103187047654,0.750519755601457,1]
["Solyc12g095900","SL3.0ch12",65992712,65994712,"-",32,293,73,296,9.846,19.783,9.9370439858245,0.00167935253587411,-0.203112801823527,4.9156312917993,0.494468436323935,1]
["Solyc12g095910","SL3.0ch12",65992274,65994274,"+",35,497,74,452,6.579,14.068,7.4894936962177,0.000512664579915686,0.075553028823448,7.96973877562186,0.778337011851416,1]
["Solyc12g095920","SL3.0ch12",66004479,66006479,"-",141,358,226,419,28.257,35.039,6.7822466638704,0.0423626773650793,-0.164927109693869,4.981318384087,0.588474500010743,1]
["Solyc12g096000","SL3.0ch12",66069725,66071725,"-",512,496,772,413,50.794,65.148,14.354028531244,3.18688445852371e-10,0.34316910504375,8.34712113923145,0.185879262347601,0.775610062488217]
["Solyc12g096010","SL3.0ch12",66078212,66080212,"-",542,304,680,167,64.066,80.283,16.217159157198,3.17280971294399e-12,0.388526603935604,2.58814266007578,0.425336021156445,1]
["Solyc12g096040","SL3.0ch12",66100925,66102925,"-",139,514,183,416,21.286,30.551,9.2645475997515,0.00135417970439976,-0.0184149015690895,4.19756871392804,0.95515874380751,1]
["Solyc12g096430","SL3.0ch12",66344617,66346617,"-",1047,171,1272,154,85.961,89.201,3.2399698768127,0.0361864250873109,0.454945160853012,-0.111257441783025,0.524387621132281,1]
["Solyc12g096440","SL3.0ch12",66345184,66347184,"+",1284,112,1579,92,91.977,94.494,2.5172374176711,0.019346987860648,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g096450","SL3.0ch12",66347984,66349984,"+",153,147,248,161,51,60.636,9.6356968215159,0.0337013011555622,-0.142378941001486,5.24549365539456,0.637784793770586,1]
["Solyc12g096660","SL3.0ch12",66458534,66460534,"+",29,316,30,156,8.406,16.129,7.7232351566152,0.0277020586088304,-1.02477634755231,0.709178899837107,0.084556373967137,0.511744904239688]
["Solyc12g096820","SL3.0ch12",66564631,66566631,"+",583,355,766,342,62.154,69.134,6.9800558835528,0.00493902597296699,-1.88937653383933,2.58513192743009,8.51511785989408E-4,0.0208038753833806]
["Solyc12g096850","SL3.0ch12",66592796,66594796,"-",760,324,1052,326,70.111,76.343,6.2318242921181,0.00291162489053889,-5.12548240610387e-15,-3.79683296932688,1,1]
["Solyc12g096870","SL3.0ch12",66601818,66603818,"+",509,572,603,532,47.086,53.128,6.0417218516058,0.0175470001060074,-4.47069703301324,3.7206554186601,0.0268142977483557,0.255213890863009]
["Solyc12g098180","SL3.0ch12",66787244,66789244,"+",405,202,576,65,66.722,89.86,23.138012835176,5.26768281045091e-22,0.282378314356576,-1.11831569942161,0.87544168071254,1]
["Solyc12g098250","SL3.0ch12",66826054,66828054,"-",721,587,913,485,55.122,65.308,10.185258101351,1.1304627607061E-6,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g098400","SL3.0ch12",66897945,66899945,"+",917,353,1098,329,72.205,76.945,4.7399146935645,0.0179627124201971,-1.30429073596278,-1.37133092752664,0.462086713451037,1]
["Solyc12g098610","SL3.0ch12",67034388,67036388,"-",164,159,222,134,50.774,62.36,11.585556753748,0.0100572326998156,1.2168400668353,1.35783807480596,0.252869644460971,0.89613738229007]
["Solyc12g098920","SL3.0ch12",67263883,67265883,"-",368,241,477,150,60.427,76.077,15.649625631477,7.69689994086783e-08,-0.0448245186267725,4.23972610830657,0.906944391404238,1]
["Solyc12g099000","SL3.0ch12",67300163,67302163,"-",92,598,109,415,13.333,20.802,7.4681933842239,0.00310330514234582,0.67701277026643,7.93485967933462,0.0419206568492824,0.338545507831369]
["Solyc12g099150","SL3.0ch12",67388430,67390430,"-",830,621,921,560,57.202,62.188,4.9857813024243,0.0202318155076016,-5.12548240610387e-15,-3.87399169536477,1,1]
["Solyc12g099210","SL3.0ch12",67415710,67417710,"+",10,396,28,432,2.463,6.087,3.623902334547,0.0345456564519022,-0.674572257652138,0.839649189830102,0.246834506888381,0.884091617103798]
["Solyc12g099270","SL3.0ch12",67455648,67457648,"-",307,244,335,162,55.717,67.404,11.687548156452,0.000745187072346412,-0.618060128577522,6.00857272405455,0.0689649145818559,0.458170942171915]
["Solyc12g099280","SL3.0ch12",67454495,67456495,"+",302,226,334,157,57.197,68.024,10.827470221564,2.10849804134798E-3,-0.508765907328333,3.91819229589415,0.196676941189925,0.796597900482353]
["Solyc12g099300","SL3.0ch12",67474325,67476325,"+",303,468,387,457,39.3,45.853,6.5534696737787,0.0273927070310977,3.71459543564816,-3.42511387267245,0.351536602470616,1]
["Solyc12g099310","SL3.0ch12",67481789,67483789,"-",28,227,78,171,10.98,31.325,20.344909047956,3.04311779903839E-7,-0.139841148699739,7.46176055500995,0.664789918851188,1]
["Solyc12g099320","SL3.0ch12",67499509,67501509,"-",765,291,878,234,72.443,78.957,6.5136527141923,2.42895939540418E-3,-0.31184139290288,5.63769944267282,0.224431979587758,0.84656010250198]
["Solyc12g099540","SL3.0ch12",67641984,67643984,"-",134,107,201,60,55.602,77.011,21.409834501836,5.9653313058873e-06,1.97216476816351,0.246625329534406,0.069710554608431,0.461320770444362]
["Solyc12g099580","SL3.0ch12",67662948,67664948,"+",518,318,740,346,61.962,68.14,6.1782406795492,0.0175470001060074,0.47230347344247,-0.341522734793326,0.69894324081972,1]
["Solyc12g099630","SL3.0ch12",67679417,67681417,"+",182,131,218,49,58.147,81.648,23.500975218676,1.67604517941719e-08,0.324401913708402,1.87374492177816,0.53779616394611,1]
["Solyc12g099790","SL3.0ch12",67767903,67769903,"+",87,166,171,217,34.387,44.072,9.6848131697975,0.0456376066456726,0.151840499250776,0.767000589637595,0.815331543022577,1]
["Solyc12g099930","SL3.0ch12",67861697,67863697,"+",121,561,183,542,17.742,25.241,7.4994438264739,3.70395134359111E-3,0.534545566261809,5.73055490486814,0.31022533465705,0.984369876122769]
["Solyc12g100070","SL3.0ch12",67931171,67933171,"-",826,686,950,628,54.63,60.203,5.5731587100408,0.00753966131685856,-0.300181730711587,3.53694173887021,0.363566986044835,1]
["Solyc12g100100","SL3.0ch12",67934890,67936890,"+",459,353,544,251,56.527,68.428,11.900579359916,1.19535014027831E-5,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g100340","SL3.0ch12",68086246,68088246,"-",710,189,940,173,78.977,84.456,5.4797833671635,0.0070437185320322,-5.12548240610387e-15,-3.91085760741443,1,1]

{"sheet":"PHYB1B2_vs_WT_IG_hypomethylated","index":4,"n_rows":2662,"n_cols":17,"rows_kept":2662}
["Supplementary Table 13. Total differentially methylated promoters (DMPs) in CHG context"]
["ID","chr","from","to","strand","met_WT","unmet_WT","met_PHYB1B2","unmet_PHYB1B2","X.met_WT","X.met_PHYB1B2","X.diff_PHYB1B2.ctrl","FDR_diff_PHYB1B2.WT","logFC_PHYB1B2","logCPM_PHYB1B2","PValue_PHYB1B2","padj_PHYB1B2"]
["Solyc00g005050","SL3.0ch00",575385,577385,"-",934,219,815,303,81.006,72.898,-8.1080389184627,3.11917380555942E-5,0.387644440774646,6.25879772751795,0.142048742271533,1]
["Solyc00g005430","SL3.0ch00",2358571,2360571,"-",624,232,394,214,72.897,64.803,-8.0945646827349,0.00319603287725079,-5.12548240610387e-15,-3.65100820910541,1,1]
["Solyc00g005440","SL3.0ch00",2365409,2367409,"-",1053,218,907,325,82.848,73.62,-9.2280211920259,2.0342431039719E-7,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g006680","SL3.0ch00",5629656,5631656,"+",13652,2749,1106,594,83.239,65.059,-18.180003371387,6.99729064082448e-63,-1.58147430974479,-3.31507523247684,0.5532990675680171,1]
["Solyc00g007970","SL3.0ch00",6941525,6943525,"-",115,4,98,25,96.639,79.675,-16.963858714217,0.000193472215442852,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g008140","SL3.0ch00",7121907,7123907,"-",100,14,220,64,87.719,77.465,-10.25450951322,0.0451008973578498,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g008570","SL3.0ch00",7584122,7586122,"-",328382,46121,14722,5359,87.685,73.313,-14.371662830678,0,-0.00547514378687348,4.3254472958713,0.994264661359307,1]
["Solyc00g008580","SL3.0ch00",7582182,7584182,"+",143697,30050,7962,3969,82.705,66.734,-15.971018464402,0,-0.179712988461231,5.85972231049318,0.777965643223827,1]
["Solyc00g009760","SL3.0ch00",8404083,8406083,"+",5279,717,1066,311,88.042,77.415,-10.627358447147,8.51886320147554E-21,-0.2212310880653,4.48675295557097,0.70675244836083,1]
["Solyc00g010530","SL3.0ch00",8854847,8856847,"-",33109,7733,2662,971,81.066,73.273,-7.7932821295867,3.35238377464783e-26,-0.128590065141809,-2.83968867727814,1,1]
["Solyc00g011150","SL3.0ch00",9131088,9133088,"-",79007,14824,5219,2955,84.201,63.849,-20.352594495457,0,-0.182470806741523,4.09570081690159,0.752088708796356,1]
["Solyc00g011160","SL3.0ch00",9129189,9131189,"+",268110,20319,10101,2252,92.955,81.77,-11.185674735286,0,-0.233163487928497,5.13575323511232,0.691237241242268,1]
["Solyc00g012430","SL3.0ch00",9551103,9553103,"+",97189,10458,5217,2097,90.285,71.329,-18.955954561568,0,-0.0166134891248842,0.15022702524476,1,1]
["Solyc00g012440","SL3.0ch00",9563323,9565323,"+",1672,727,376,210,69.696,64.164,-5.5318840187962,0.0240345580064483,-0.82017840187081,2.48019316520533,0.220357146711844,1]
["Solyc00g013186","SL3.0ch00",9906680,9908680,"+",801,224,594,214,78.146,73.515,-4.6314899782661,0.0434372678816859,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g015600","SL3.0ch00",10265463,10267463,"-",1020,102,758,113,90.909,87.026,-3.8826844796994,0.0161111323971419,-5.12548240610387e-15,-3.7935098886122,1,1]
["Solyc00g017235","SL3.0ch00",10541075,10543075,"+",344,79,347,122,81.324,73.987,-7.3366702455302,0.0220594412317232,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g017540","SL3.0ch00",10558570,10560570,"+",220,107,161,143,67.278,52.961,-14.317761145984,0.000945964445374797,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g030215","SL3.0ch00",11647547,11649547,"-",569,16,667,49,97.265,93.156,-4.1085326839517,2.50450581472582E-3,-5.12548240610387e-15,-3.76187476156875,1,1]
["Solyc00g032947","SL3.0ch00",11830799,11832799,"-",60,28,4,10,68.182,28.571,-39.61038961039,0.0157911419120139,-5.12548240610387e-15,-3.57533435268597,1,1]
["Solyc00g036960","SL3.0ch00",12027754,12029754,"-",183,11,160,28,94.33,85.106,-9.2235139284931,9.49740273053736E-3,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g047180","SL3.0ch00",12551302,12553302,"-",233,12505,125,9223,1.829,1.337,-0.49198813008533,0.0106591115886949,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g047190","SL3.0ch00",12550418,12552418,"+",327,16285,180,11295,1.968,1.569,-0.39982908646242,0.0281938410397239,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g060810","SL3.0ch00",13198111,13200111,"-",43,28,24,42,60.563,36.364,-24.199743918054,0.0145593249800039,4.6153134199843,7.62727542464885,4.40104973351248e-05,5.74463094714268E-3]
["Solyc00g068970","SL3.0ch00",13555018,13557018,"-",3431,358,400,117,90.552,77.369,-13.182157655802,8.8325151519037e-15,-0.530865190191854,4.99671965056755,0.364852504189297,1]
["Solyc00g068980","SL3.0ch00",13553285,13555285,"+",67662,12656,4862,2310,84.243,67.791,-16.451224480848,1.65560758836796e-232,0.125660466252744,2.42877767015063,0.868719884876826,1]
["Solyc00g071180","SL3.0ch00",13651920,13653920,"-",811,523,694,598,60.795,53.715,-7.0794324200129,0.00104838748327509,9.80250579362967,-0.604256039558963,0.000383713914618874,0.0303643347302829]
["Solyc00g090870","SL3.0ch00",14449470,14451470,"-",930,278,631,283,76.987,69.037,-7.9495558421609,0.000209730926244608,0.375143100564807,2.38533792411707,0.356295824103205,1]
["Solyc00g094520","SL3.0ch00",14585676,14587676,"-",568,24580,369,18900,2.259,1.915,-0.3436359228844,0.0260417398937478,5.41298518866233,-2.96074051384601,0.0446753442622108,0.649161791662578]
["Solyc00g094530","SL3.0ch00",14586705,14588705,"-",609,26027,378,19709,2.286,1.882,-0.4045652276092,0.00747751258907913,3.46363352561052,-2.86231287498452,0.334098577915024,1]
["Solyc00g099580","SL3.0ch00",14780831,14782831,"-",1404,472,1295,634,74.84,67.133,-7.7068556351767,1.40015641748995E-6,-3.70634268122269,-3.48102496397314,0.470003531382676,1]
["Solyc00g112490","SL3.0ch00",15235729,15237729,"+",2882,267,2688,317,91.521,89.451,-2.0702026737485,0.0144421445375277,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g125980","SL3.0ch00",15682094,15684094,"+",447,8417,230,5739,5.043,3.853,-1.1896282870644,2.15817763291746E-3,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g125990","SL3.0ch00",15682094,15684094,"+",447,8417,230,5739,5.043,3.853,-1.1896282870644,2.15817763291746E-3,0.344161833840133,-0.333440414084136,0.716577160232107,1]
["Solyc00g129880","SL3.0ch00",15807077,15809077,"+",424,138,430,189,75.445,69.467,-5.9779577897999,0.0420905866990901,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g129980","SL3.0ch00",15812774,15814774,"-",683,101,279,67,87.117,80.636,-6.4815087884865,0.0149328865824922,-5.12548240610387e-15,-3.91085760741443,1,1]
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["Solyc12g099230","SL3.0ch12",67416972,67418972,"+",218,613,129,551,26.233,18.971,-7.2628654349827,0.00284660446511313,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g099310","SL3.0ch12",67481789,67483789,"-",168,226,154,357,42.64,30.137,-12.50260760726,0.000482821924156731,0.333762539957584,7.46176055500995,0.302033870505285,1]
["Solyc12g099440","SL3.0ch12",67569779,67571779,"+",248,239,210,322,50.924,39.474,-11.450340430131,0.000967013493179329,0.257087362063916,8.34987954611291,0.3773860331822,1]
["Solyc12g099470","SL3.0ch12",67596659,67598659,"-",473,627,307,576,43,34.768,-8.2321630804077,0.000826152980428875,0.439458527466112,6.04285080568767,0.101896515927061,0.903865857426428]
["Solyc12g099490","SL3.0ch12",67600934,67602934,"+",787,357,788,435,68.794,64.432,-4.3619810279663,0.0471547539570957,0.41894066509801,6.299373887455,0.153857555533887,1]
["Solyc12g099500","SL3.0ch12",67608122,67610122,"-",186,713,134,713,20.69,15.821,-4.8691120791434,0.0205526760123294,0.410258324904084,7.35397338436693,0.294692063095923,1]
["Solyc12g099900","SL3.0ch12",67825277,67827277,"+",141,927,118,1179,13.202,9.098,-4.1043289180737,0.00525384586935964,0.738912728584122,4.02006486106073,0.117955204775644,0.9565293775279]
["Solyc12g099995","SL3.0ch12",67891579,67893579,"+",20,260,7,251,7.143,2.713,-4.4296788482835,0.0496958111180485,-0.0243741281871876,2.5729533890001,0.963549002535771,1]
["Solyc12g100140","SL3.0ch12",67956977,67958977,"+",144,447,103,457,24.365,18.393,-5.9726250906454,0.0295627280864748,-0.0922476795799359,3.81081318018535,0.800909009470455,1]
["Solyc12g100310","SL3.0ch12",68065572,68067572,"-",517,463,480,546,52.755,46.784,-5.9714763098222,0.0188504225412193,-0.0548640505556723,5.72997225902678,0.858519154181172,1]

{"sheet":"PHYB1B2_vs_WT_IG_hypermethylate","index":5,"n_rows":9684,"n_cols":17,"rows_kept":4500,"cut":true,"bounds":{"rows_first":2000,"rows_last":500,"rows_between":2000,"halvings":0}}
["Supplementary Table 13. Total differentially methylated promoters (DMPs) in CHG context"]
["ID","chr","from","to","strand","met_WT","unmet_WT","met_PHYB1B2","unmet_PHYB1B2","X.met_WT","X.met_PHYB1B2","X.diff_PHYB1B2.ctrl","FDR_diff_PHYB1B2.WT","logFC_PHYB1B2","logCPM_PHYB1B2","PValue_PHYB1B2","padj_PHYB1B2"]
["Solyc00g005000","SL3.0ch00",14479,16479,"+",432,926,442,778,31.811,36.23,4.4180207151307,0.0374054878944729,4.71479458307379,-2.90243574957455,0.0471469025131507,0.662178706002876]
["Solyc00g005084","SL3.0ch00",807592,809592,"+",873,230,770,157,79.148,83.064,3.9158673853108,0.0482220573464782,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g005096","SL3.0ch00",1732561,1734561,"+",877,346,975,275,71.709,78,6.2910874897792,1.27127501770461E-3,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g006510","SL3.0ch00",4370359,4372359,"+",50,33,131,30,60.241,81.366,21.125495771907,2.04944956140631E-3,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g006540","SL3.0ch00",4386391,4388391,"-",590,139,871,152,80.933,85.142,4.2089553439613,0.0418218235143472,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g006650","SL3.0ch00",5617777,5619777,"-",423,205,651,218,67.357,74.914,7.5570060029465,0.00485396050806213,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g006660","SL3.0ch00",5628502,5630502,"+",168,83,225,41,66.932,84.586,17.654195249079,1.82700913453838e-05,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g006805","SL3.0ch00",5780749,5782749,"-",1284,207,968,107,86.117,90.047,3.9298114266997,0.0074235135768259,0.764814205640683,-2.36691828856068,0.741986104167052,1]
["Solyc00g006820","SL3.0ch00",5819900,5821900,"+",682,624,919,672,52.221,57.762,5.5418929025539,0.00801456828045216,0.230064066099273,1.61308375064248,0.789337964976326,1]
["Solyc00g006867","SL3.0ch00",6390079,6392079,"+",35,859,213,745,3.915,22.234,18.318831644973,8.16699733192319e-32,2.22969991726051,-0.558251759538668,0.0146960067334165,0.354946628498543]
["Solyc00g006870","SL3.0ch00",6404880,6406880,"+",928,626,987,506,59.717,66.109,6.3916466461677,0.00102592180196417,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g006880","SL3.0ch00",6433744,6435744,"+",447,130,447,79,77.47,84.981,7.511317882584,0.00466839029642495,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g007550","SL3.0ch00",6650039,6652039,"-",285,354,373,334,44.601,52.758,8.1571939890166,0.00838747762002456,-1.07853177534438,-3.43052628147651,0.678036194447422,1]
["Solyc00g007920","SL3.0ch00",6890411,6892411,"-",452,93,355,44,82.936,88.972,6.0366512611805,0.0241339506952926,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g008110","SL3.0ch00",7099931,7101931,"-",307,81,241,33,79.124,87.956,8.8324930393558,0.0087294307124333,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g008165","SL3.0ch00",7190282,7192282,"+",171,39,142,15,81.429,90.446,9.01728844404,0.0336491464639409,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g009020","SL3.0ch00",7793998,7795998,"+",1087,316,1366,210,77.477,86.675,9.1982915507379,6.8205001129502e-10,0.278158155018222,7.62400916820391,0.278495647053144,1]
["Solyc00g009050","SL3.0ch00",7822149,7824149,"-",1773,609,2256,270,74.433,89.311,14.87791452521,1.14014489796059e-40,1.11039515972238,-1.83143939226503,0.317251340345003,1]
["Solyc00g009110","SL3.0ch00",7871111,7873111,"+",38,1136,203,1300,3.237,13.506,10.269523417674,1.57289714521902e-20,-0.205033819553407,3.27195840491963,0.746454350338644,1]
["Solyc00g009765","SL3.0ch00",8624891,8626891,"+",275,160,511,154,63.218,76.842,13.62371445856,7.99570049270082e-06,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g011175","SL3.0ch00",9159658,9161658,"+",284,150,171,54,65.438,76,10.562211981567,0.0139692917430292,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g011880","SL3.0ch00",9382471,9384471,"+",1087,152,1341,135,87.732,90.854,3.1216165672553,0.0219723860298217,-0.087980976700484,3.70833791061402,0.817352397013646,1]
["Solyc00g011890","SL3.0ch00",9403098,9405098,"-",465,593,564,580,43.951,49.301,5.3498486390736,0.0271676472435576,0.328594040245501,7.36530330208955,0.319306525808668,1]
["Solyc00g012700","SL3.0ch00",9627415,9629415,"-",928,331,758,182,73.709,80.638,6.9290047825867,6.37042973829491E-4,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g013110","SL3.0ch00",9719089,9721089,"-",258,2069,237,1322,11.087,15.202,4.1148158122583,0.000739222958319382,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g013120","SL3.0ch00",9726388,9728388,"-",326,1445,403,986,18.408,29.014,10.605999628443,4.14914751897817e-11,2.62933817805086,-3.04179885224491,0.248626347397042,1]
["Solyc00g013130","SL3.0ch00",9727452,9729452,"-",619,6143,854,4107,9.154,17.214,8.0601748950897,3.59954384135247e-36,-5.12548240610387e-15,-3.50606629457688,1,1]
["Solyc00g013133","SL3.0ch00",9727784,9729784,"-",855,7903,1130,5340,9.763,17.465,7.7027212567498,1.00959871955573e-41,4.23070641458516,-3.38388112100868,0.192979777145457,1]
["Solyc00g013137","SL3.0ch00",9730078,9732078,"-",426,1277,401,736,25.015,35.268,10.253569803611,5.6944062818522E-8,-5.12548240610387e-15,-3.78951150766205,1,1]
["Solyc00g013140","SL3.0ch00",9737602,9739602,"-",1587,17802,1455,13051,8.185,10.03,1.8452788955165,4.74999510039685e-08,-2.08691567044056,-1.03249406421298,0.0443678338197427,0.647469881707286]
["Solyc00g013150","SL3.0ch00",9736648,9738648,"+",1524,26425,1527,18999,5.453,7.439,1.9865562121444,2.79585179212501E-17,-1.37219645170678,-2.82133188471744,0.722735583979428,1]
["Solyc00g013155","SL3.0ch00",9739388,9741388,"-",641,7965,579,5723,7.448,9.188,1.7392676155396,0.000561832808033013,0.6586499955724,-3.15174374011737,1,1]
["Solyc00g013160","SL3.0ch00",9741809,9743809,"-",1255,16184,1082,10285,7.197,9.519,2.3222688788402,4.40908220435849e-11,0.686873034965411,-1.09183566663966,0.49980637344463,1]
["Solyc00g013170","SL3.0ch00",9740381,9742381,"+",1221,14418,1061,10123,7.807,9.487,1.6793622442189,8.51995930617607e-06,2.49816678416325,-1.39935424343059,0.0498393013926367,0.679105574175935]
["Solyc00g013180","SL3.0ch00",9744467,9746467,"-",1115,14587,999,8171,7.101,10.894,3.7932140422901,8.42037256056083e-23,-0.0967806950976726,-2.8354164280273,1,1]
["Solyc00g013183","SL3.0ch00",9797940,9799940,"-",517,168,580,113,75.474,83.694,8.2196311393392,0.0006939351491518,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g014170","SL3.0ch00",9966728,9968728,"+",640,391,601,279,62.076,68.295,6.2197998412838,0.011378863673484,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g014290","SL3.0ch00",10010691,10012691,"-",916,198,779,112,82.226,87.43,5.2036422473287,0.0044411627944588,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g014395","SL3.0ch00",10046778,10048778,"+",1497,519,1553,438,74.256,78.001,3.7450521393892,0.0132252382534177,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g014830","SL3.0ch00",10125614,10127614,"-",281,16986,248,11480,1.627,2.115,0.48721583356055,0.00732768220749336,-2.42859430503842,-1.51507708153946,0.0805661738359253,0.829673474774646]
["Solyc00g014840","SL3.0ch00",10123786,10125786,"+",238,18475,220,12678,1.272,1.706,0.43384770105125,0.00523773250831706,1.82001064977851,-3.38395309736054,0.999999999999999,1]
["Solyc00g014860","SL3.0ch00",10128237,10130237,"-",214,18213,181,12063,1.161,1.478,0.31693573449199,0.0338524530567615,-5.12548240610387e-15,-3.87428074584103,1,1]
["Solyc00g015000","SL3.0ch00",10152463,10154463,"-",73,172,70,103,29.796,40.462,10.666509378318,0.049580324731765,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g015737","SL3.0ch00",10361092,10363092,"-",1678,628,1433,441,72.767,76.467,3.7007537295404,0.0156728228005149,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g017760","SL3.0ch00",10585381,10587381,"-",3503,1095,3207,842,76.185,79.205,3.0194439559502,0.00254143989278349,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g019620","SL3.0ch00",10819131,10821131,"-",1109,10037,1090,7818,9.95,12.236,2.2864344261668,2.26061173060887e-06,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g019630","SL3.0ch00",10819968,10821968,"-",3176,45093,2572,27687,6.58,8.5,1.9201580146217,8.24683922907969e-22,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g019730","SL3.0ch00",10829313,10831313,"-",1292,16070,1242,13566,7.442,8.387,0.94581919156144,0.00497326123939805,-0.0664167606197044,-2.03310401875312,1,1]
["Solyc00g019740","SL3.0ch00",10830415,10832415,"-",1576,21894,1729,19010,6.715,8.337,1.6219944462424,1.38775637994468E-9,0.465456498500766,-1.30025223554522,0.804013717040859,1]
["Solyc00g019750","SL3.0ch00",10831749,10833749,"-",568,6714,666,5304,7.8,11.156,3.3557239645081,5.89703531499484e-10,1.82306865567003,-3.27883722145106,1,1]
["Solyc00g020010","SL3.0ch00",10853344,10855344,"-",1517,20927,1361,13670,6.759,9.055,2.2955757175087,1.17484292444343E-14,-5.12548240610387e-15,-3.39344519584705,1,1]
["Solyc00g020020","SL3.0ch00",10851713,10853713,"+",419,24114,382,17475,1.708,2.139,0.4313134737418,0.00435626823658223,-5.25509700125184,-3.05381982949616,0.0458080309623468,0.654252856789912]
["Solyc00g020030","SL3.0ch00",10854853,10856853,"-",1513,20002,1421,14852,7.032,8.732,1.699952839592,1.32785366459203E-8,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g020040","SL3.0ch00",10854013,10856013,"+",2035,24734,1830,17225,7.602,9.604,2.0017015064177,7.76050179190629e-13,3.11085702039094,-2.82130233030166,0.420369770642619,1]
["Solyc00g020540","SL3.0ch00",10903182,10905182,"+",1191,351,1458,311,77.237,82.419,5.1820919290945,0.00082095908649656,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g020545","SL3.0ch00",10945268,10947268,"+",7537,4731,4055,1770,61.436,69.614,8.1774769769847,2.19780337418049e-25,0.7479794178609,-3.07629557896507,0.810958385656914,1]
["Solyc00g020940","SL3.0ch00",10946755,10948755,"+",9117,4744,4815,2292,65.774,67.75,1.975630383666,0.0107387819102687,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g023470","SL3.0ch00",11174287,11176287,"+",1804,443,2040,419,80.285,82.961,2.6757288602959,0.0369289011770132,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g023710","SL3.0ch00",11199671,11201671,"-",434,7567,461,5258,5.424,8.061,2.6365278391609,1.06865790474904e-08,-5.12548240610387e-15,-3.87428074584103,1,1]
["Solyc00g024040","SL3.0ch00",11224494,11226494,"-",321,448,460,347,41.743,57.001,15.258716400546,1.55936163748333e-08,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g024150","SL3.0ch00",11224558,11226558,"+",327,639,468,496,33.851,48.548,14.696786165305,8.50944822353395e-10,-0.753257827049312,5.42107019365619,0.024135421119797,0.476405755397505]
["Solyc00g024570","SL3.0ch00",11259566,11261566,"+",4735,1207,5207,1107,79.687,82.468,2.7805583847321,3.73373686102824E-4,-3.64129363446094,-3.7595815468704,0.440723646992473,1]
["Solyc00g025290","SL3.0ch00",11313892,11315892,"+",861,11914,1078,7891,6.74,12.019,5.279451138396,1.84162233411317E-38,-1.04819620316958,-1.17447558515912,0.624792945762385,1]
["Solyc00g025300","SL3.0ch00",11317263,11319263,"-",1263,15768,1090,9791,7.416,10.017,2.6015729567697,7.55265716752913e-13,-5.12548240610387e-15,-3.77033964572029,1,1]
["Solyc00g027770","SL3.0ch00",11475330,11477330,"+",686,78,699,52,89.791,93.076,3.2853228853675,0.0488146654585532,0.0877950452051471,6.00804120453292,0.744865876102621,1]
["Solyc00g028550","SL3.0ch00",11530930,11532930,"-",224,245,396,194,47.761,67.119,19.357450037946,3.54217606910156e-09,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g028560","SL3.0ch00",11532006,11534006,"-",564,296,749,261,65.581,74.158,8.5770204927469,0.000271945823478031,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g028760","SL3.0ch00",11537778,11539778,"+",1716,409,1943,316,80.753,86.012,5.258568341015,1.74057031945238E-5,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc00g030000","SL3.0ch00",11624489,11626489,"-",549,921,1215,896,37.347,57.556,20.208722048744,5.15897316338083e-31,-5.12548240610387e-15,-3.47695362856055,1,1]
["Solyc00g030100","SL3.0ch00",11623845,11625845,"+",1118,876,2242,1214,56.068,64.873,8.8044805713437,1.98434277806583e-09,-5.12548240610387e-15,-3.62703845704372,1,1]
["Solyc00g030820","SL3.0ch00",11677156,11679156,"-",701,576,966,622,54.894,60.831,5.936950780028,0.004141686268976,0.0896755431640802,-2.52453426152791,1,1]
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["Solyc12g096960","SL3.0ch12",66643219,66645219,"+",1891,690,2584,753,73.266,77.435,4.1686457953206,0.000849684399268681,1.75012294082769,1.97820963276441,0.227494307962447,1]
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["Solyc12g098100","SL3.0ch12",66729036,66731036,"+",406,310,460,212,56.704,68.452,11.748470337856,3.90202913773814E-5,-1.21571080377868,-3.60253566581618,0.795122463652444,1]
["Solyc12g098130","SL3.0ch12",66744792,66746792,"-",557,579,672,507,49.032,56.997,7.9657653298928,0.000524279903995098,-6.11898592151213,0.410233964066996,0.000680583515541569,0.0463678308264587]
["Solyc12g098170","SL3.0ch12",66785414,66787414,"+",188,459,210,387,29.057,35.176,6.1186923799834,0.0443717673015872,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g098180","SL3.0ch12",66787244,66789244,"+",384,176,554,77,68.571,87.797,19.225718813674,1.03495650988154E-14,2.24628093373859,-1.11831569942161,0.194853982968509,1]
["Solyc12g098230","SL3.0ch12",66819626,66821626,"-",830,590,1086,394,58.451,73.378,14.927674153026,5.08968131231043e-16,-1.98205371409533,-2.58167663204452,0.14455426533223,1]
["Solyc12g098240","SL3.0ch12",66822209,66824209,"-",42,139,73,126,23.204,36.683,13.478997195924,0.0125213658687347,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g098250","SL3.0ch12",66826054,66828054,"-",691,625,897,617,52.508,59.247,6.7394289568887,1.28461368520762E-3,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g098320","SL3.0ch12",66858577,66860577,"-",156,155,138,70,50.161,66.346,16.185382141974,0.00109359291638229,-5.39733667370813,-1.26208373412179,0.00990264325931125,0.283131689927294]
["Solyc12g098330","SL3.0ch12",66857687,66859687,"+",259,239,281,184,52.008,60.43,8.4220753983676,0.0206410491395449,0.361648409919459,6.82266978338076,0.26696112579058,1]
["Solyc12g098460","SL3.0ch12",66934807,66936807,"+",314,570,678,613,35.52,52.517,16.997066359166,1.0949339897626E-13,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g098470","SL3.0ch12",66954625,66956625,"-",455,297,519,257,60.505,66.881,6.3761241500329,0.0228555568261667,-0.177060699370575,-0.319748805419847,0.828856036442058,1]
["Solyc12g098510","SL3.0ch12",66975596,66977596,"-",610,411,705,372,59.745,65.46,5.7142623295202,0.0175329116572322,0.287270877149122,3.37595498466805,0.46839139277055303,1]
["Solyc12g098590","SL3.0ch12",67025243,67027243,"+",852,495,948,458,63.252,67.425,4.1736496782799,0.0415699063490246,1.19065458410669,-3.68964036006616,0.728595078118171,1]
["Solyc12g098670","SL3.0ch12",67075727,67077727,"+",361,467,482,355,43.599,57.587,13.987585060516,1.17950735623247E-7,-0.418282661990245,4.31489245306894,0.309383325236271,1]
["Solyc12g098740","SL3.0ch12",67124328,67126328,"+",46,238,198,258,16.197,43.421,27.223869532987,1.14966517430365E-13,0.407494895449184,7.91005035557334,0.157628122488508,1]
["Solyc12g098750","SL3.0ch12",67138754,67140754,"-",107,447,182,469,19.314,27.957,8.6429098249292,0.00186034726780469,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g098790","SL3.0ch12",67160582,67162582,"-",134,151,245,143,47.018,63.144,16.126786037258,0.00019548157873783,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g098800","SL3.0ch12",67161513,67163513,"+",136,212,248,172,39.08,59.048,19.967159277504,4.21296357252741e-07,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g098820","SL3.0ch12",67171113,67173113,"+",778,451,1018,475,63.303,68.185,4.8813639130698,0.0185375566817887,0.125112559423814,6.12133235883969,0.636887467887174,1]
["Solyc12g099060","SL3.0ch12",67328157,67330157,"+",52,614,98,629,7.808,13.48,5.6722472128249,0.00233963563765098,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g099070","SL3.0ch12",67331543,67333543,"+",643,284,827,293,69.364,73.839,4.4757474187086,0.047398659859363,4.4449061454631,-3.5715005195899,0.183623266604457,1]
["Solyc12g099090","SL3.0ch12",67340163,67342163,"+",114,513,90,215,18.182,29.508,11.326378539493,0.000556742157204063,0.0114756366505144,5.55210792992616,0.968883695383,1]
["Solyc12g099150","SL3.0ch12",67388430,67390430,"-",1281,540,1422,395,70.346,78.261,7.9149058090395,4.70374237758048e-07,-1.82366189940705,-3.87399169536477,0.999999999999999,1]
["Solyc12g099170","SL3.0ch12",67396065,67398065,"+",408,471,491,351,46.416,58.314,11.897156939839,5.70115073436166e-06,-0.257615013856618,2.43600541217631,0.610509053083561,1]
["Solyc12g099175","SL3.0ch12",67397335,67399335,"+",271,461,359,300,37.022,54.476,17.454621590918,1.12305743489121e-09,0.155628348307017,2.62439032715876,0.729314635596627,1]
["Solyc12g099220","SL3.0ch12",67421279,67423279,"-",764,548,796,419,58.232,65.514,7.2826959751079,0.000753218129074588,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g099270","SL3.0ch12",67455648,67457648,"-",315,573,346,326,35.473,51.488,16.015122265122,3.10861877793323E-9,-0.50235819394012,6.00857272405455,0.137726871385673,1]
["Solyc12g099290","SL3.0ch12",67474851,67476851,"-",340,364,447,363,48.295,55.185,6.8897306397306,0.0190992459291893,-0.369480189556119,2.95743426434154,0.385343842923453,1]
["Solyc12g099300","SL3.0ch12",67474325,67476325,"+",339,758,444,495,30.902,47.284,16.381883789947,7.93042106846468e-13,0.341998429138389,-3.42511387267245,1,1]
["Solyc12g099330","SL3.0ch12",67503363,67505363,"-",230,602,245,428,27.644,36.404,8.7599297062521,1.07373859919394E-3,0.388875882438261,6.74897606902199,0.263448086764015,1]
["Solyc12g099390","SL3.0ch12",67534610,67536610,"+",268,246,417,190,52.14,68.699,16.558439477176,1.84155297603335e-07,0.978507278522953,6.82112596413925,1.22729563307834E-3,0.0718460068804356]
["Solyc12g099570","SL3.0ch12",67654896,67656896,"+",1198,214,1433,190,84.844,88.293,3.4490914073368,0.0130040778524212,0.290501441226832,4.32609331436301,0.391450211066905,1]
["Solyc12g099580","SL3.0ch12",67662948,67664948,"+",511,447,593,415,53.34,58.829,5.489072803791,0.0317539384715794,-1.87394854496558,-0.341522734793326,0.0882712082510868,0.860070951673471]
["Solyc12g099590","SL3.0ch12",67668359,67670359,"-",194,364,211,293,34.767,41.865,7.0980542754736,0.0368240476603417,0.0170873137534619,-0.0443922890031553,0.993278741283499,1]
["Solyc12g099600","SL3.0ch12",67668528,67670528,"+",207,441,231,368,31.944,38.564,6.619829345205,0.0302104824368418,-0.146917364525077,3.96312420906162,0.681134443618757,1]
["Solyc12g099670","SL3.0ch12",67708881,67710881,"-",571,191,820,163,74.934,83.418,8.483724631064,7.76420758981454e-05,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g099680","SL3.0ch12",67708958,67710958,"+",526,187,747,152,73.773,83.092,9.3195337814964,3.74543011833294E-5,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g099710","SL3.0ch12",67720254,67722254,"+",18,366,27,157,4.688,14.674,9.9864130434783,0.00038490714226094,0.423118851378801,5.2151773837404,0.177246062450354,1]
["Solyc12g099780","SL3.0ch12",67768996,67770996,"-",69,745,103,724,8.477,12.455,3.9779969042363,0.0213932170474749,0.0541289580120932,-0.490122934462841,0.975913839903774,1]
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["Solyc12g099850","SL3.0ch12",67807817,67809817,"-",44,241,39,39,15.439,50,34.561403508772,1.57766604737043e-08,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g099910","SL3.0ch12",67830642,67832642,"+",1595,148,2005,117,91.509,94.486,2.9774409337904,0.00119489931067494,-0.0532833278507167,6.38411987643982,0.855137759915574,1]
["Solyc12g100035","SL3.0ch12",67914214,67916214,"-",868,710,911,626,55.006,59.271,4.2649706067405,0.0331601237780347,-5.12548240610387e-15,-3.91085760741443,1,1]
["Solyc12g100040","SL3.0ch12",67922372,67924372,"-",247,856,212,537,22.393,28.304,5.9109335263579,0.0108826600891566,0.0144078598789472,4.18102588021319,0.963326903007547,1]
["Solyc12g100060","SL3.0ch12",67928818,67930818,"-",10,102,44,189,8.929,18.884,9.9555487431024,0.0342976719210708,0.653467639806831,8.07136467742816,0.0967599513911262,0.888700539814624]
["Solyc12g100210","SL3.0ch12",68000239,68002239,"+",2,135,27,288,1.46,8.571,7.11157455683,0.00798859538093435,-5.12548240610387e-15,-3.91085760741443,1,1]
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["Solyc12g100280","SL3.0ch12",68030644,68032644,"-",66,165,112,178,28.571,38.621,10.049261083744,0.037966190654755,-3.42038634112455,-3.76922177802069,0.436642576787957,1]
["Solyc12g100300","SL3.0ch12",68050958,68052958,"+",892,148,1035,128,85.769,88.994,3.2247503141742,0.0439404672456079,0.373634227887486,-1.78227665393969,0.827322954526929,1]
["Solyc12g100353","SL3.0ch12",68098699,68100699,"+",9,783,28,806,1.136,3.357,2.2209505123174,0.0070280933115522,-5.12548240610387e-15,-3.91085760741443,1,1]

{"sheet":"PHYB1B2_vs_WT_BK_hypomethylated","index":6,"n_rows":3028,"n_cols":17,"rows_kept":3028}
["Supplementary Table 13. Total differentially methylated promoters (DMPs) in CHG context"]
["ID","chr","from","to","strand","met_WT","unmet_WT","met_PHYB1B2","unmet_PHYB1B2","X.met_WT","X.met_PHYB1B2","X.diff_PHYB1B2.ctrl","FDR_diff_PHYB1B2.WT","logFC_PHYB1B2","logCPM_PHYB1B2","PValue_PHYB1B2","padj_PHYB1B2"]
["Solyc00g005050","SL3.0ch00",575385,577385,"-",839,111,815,321,88.316,71.743,-16.572831727205,1.02707001859196e-19,-0.0145324026414522,6.25879772751795,0.956543768440776,1]
["Solyc00g005283","SL3.0ch00",2354618,2356618,"-",535,108,385,124,83.204,75.639,-7.5652256276601,0.00501086941185315,0.722325688227394,-3.22628728327423,0.999999999999998,1]
["Solyc00g005440","SL3.0ch00",2365409,2367409,"-",741,166,665,276,81.698,70.67,-11.028404650569,3.04737094276179e-07,0,-3.91085760741443,1,1]
["Solyc00g005450","SL3.0ch00",2464349,2466349,"+",628,161,444,189,79.594,70.142,-9.4522432258723,0.000193069263400058,0,-3.91085760741443,1,1]
["Solyc00g006680","SL3.0ch00",5629656,5631656,"+",9978,1725,938,434,85.26,68.367,-16.892842756174,5.67942219059281e-47,2.25004503381293,-3.31507523247684,0.277680236936339,0.865886991401381]
["Solyc00g006870","SL3.0ch00",6404880,6406880,"+",705,453,752,609,60.881,55.253,-5.6273389347211,0.0108327764456496,0,-3.91085760741443,1,1]
["Solyc00g008140","SL3.0ch00",7121907,7123907,"-",178,23,57,36,88.557,61.29,-27.266891349703,1.73309077922866E-6,0,-3.91085760741443,1,1]
["Solyc00g008570","SL3.0ch00",7584122,7586122,"-",190538,25693,8341,4219,88.118,66.409,-21.708564276639,0,-0.378534275089891,4.3254472958713,0.505884165502298,1]
["Solyc00g008580","SL3.0ch00",7582182,7584182,"+",87235,14590,5364,3042,85.671,63.812,-21.859932043209,0,-0.11682368832629,5.85972231049318,0.854529952600251,1]
["Solyc00g008910","SL3.0ch00",7693875,7695875,"+",634,110,622,172,85.215,78.338,-6.8775222772948,1.88364190401787E-3,0,-3.91085760741443,1,1]
["Solyc00g009040","SL3.0ch00",7811311,7813311,"+",796,141,946,228,84.952,80.579,-4.3727580319953,0.0195977532352297,3.94485158019872,-2.81329348036956,0.217301792004393,0.76036494780015]
["Solyc00g009760","SL3.0ch00",8404083,8406083,"+",3272,458,667,157,87.721,80.947,-6.7745776829173,4.64690212722072E-6,-0.168232941700414,4.48675295557097,0.774646193865514,1]
["Solyc00g010530","SL3.0ch00",8854847,8856847,"-",18824,3075,1555,643,85.958,70.746,-15.212130086337,4.80050950703464e-65,0.28741997401247,-2.83968867727814,1,1]
["Solyc00g011150","SL3.0ch00",9131088,9133088,"-",56272,8945,4199,2591,86.284,61.841,-24.443308476247,0,-0.258431063436835,4.09570081690159,0.652360941584166,1]
["Solyc00g011160","SL3.0ch00",9129189,9131189,"+",136824,11114,5292,1826,92.487,74.347,-18.140666758894,0,-0.357182750882131,5.13575323511232,0.542047169917122,1]
["Solyc00g011170","SL3.0ch00",9132267,9134267,"-",362,201,56,56,64.298,50,-14.298401420959,0.0125543077047948,-0.0334470286899373,-2.15704237410903,1,1]
["Solyc00g011175","SL3.0ch00",9159658,9161658,"+",169,67,67,58,71.61,53.6,-18.010169491525,2.31152821146869E-3,0,-3.91085760741443,1,1]
["Solyc00g011670","SL3.0ch00",9318728,9320728,"-",234,38,197,74,86.029,72.694,-13.335684827437,0.00050615470005962,0,-3.91085760741443,1,1]
["Solyc00g012430","SL3.0ch00",9551103,9553103,"+",56783,5255,3203,1702,91.529,65.301,-26.228671657919,0,-0.0621185081505357,0.15022702524476,0.972798868732273,1]
["Solyc00g013120","SL3.0ch00",9726388,9728388,"-",232,208,205,606,52.727,25.277,-27.449837462168,3.0952638860013e-20,0,-3.04179885224491,1,1]
["Solyc00g013130","SL3.0ch00",9727452,9729452,"-",506,1006,415,2839,33.466,12.754,-20.712074353746,8.28179485263681e-58,3.57648846483742,-3.50606629457688,0.362765001155474,0.981125032992742]
["Solyc00g013133","SL3.0ch00",9727784,9729784,"-",683,1165,612,3541,36.959,14.736,-22.222539279486,5.05505331370665E-76,4.08680292371252,-3.38388112100868,0.228296090167337,0.781406177330653]
["Solyc00g013140","SL3.0ch00",9737602,9739602,"-",1244,3379,1493,8908,26.909,14.354,-12.554544591847,1.84870935906131e-69,-0.0387925789535757,-1.03249406421298,0.973819435513898,1]
["Solyc00g013150","SL3.0ch00",9736648,9738648,"+",1150,5152,1293,12764,18.248,9.198,-9.0499109724796,1.16628322963846e-68,-0.696345131618904,-2.82133188471744,0.775779565655172,1]
["Solyc00g013155","SL3.0ch00",9739388,9741388,"-",411,1323,472,3461,23.702,12.001,-11.701405109987,8.79140206813538E-26,4.1679479085352,-3.15174374011737,0.224849234112231,0.775769982224973]
["Solyc00g013160","SL3.0ch00",9741809,9743809,"-",725,2994,775,6961,19.494,10.018,-9.476390557669,9.97346942638233e-41,0.00146087661955897,-1.09183566663966,1,1]
["Solyc00g013170","SL3.0ch00",9740381,9742381,"+",731,2327,782,6127,23.905,11.319,-12.58594277225,4.60830641154851e-53,1.43203745344161,-1.39935424343059,0.203388073148631,0.735941790630273]
["Solyc00g013180","SL3.0ch00",9744467,9746467,"-",735,2158,757,5929,25.406,11.322,-14.083987063165,1.29398479733717E-61,4.10959407962949,-2.8354164280273,0.0968354756118546,0.48219564133159]
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["Solyc12g056250","SL3.0ch12",63161239,63163239,"-",637,291,784,479,68.642,62.074,-6.5678154093974,0.00423840356583179,1.04747827815836,6.03572023120816,0.00290105369795974,0.0447841556619008]
["Solyc12g056420","SL3.0ch12",63294362,63296362,"+",403,236,279,215,63.067,56.478,-6.5895598512352,0.0469423682986911,3.2811605885912,-3.59471114035487,0.515977299339697,1]
["Solyc12g056490","SL3.0ch12",63384806,63386806,"-",267,185,349,370,59.071,48.54,-10.531158073529,1.59684629412295E-3,0.68254025335584,-0.864873910004565,0.516430704720405,1]
["Solyc12g056560","SL3.0ch12",63454866,63456866,"+",40,429,15,491,8.529,2.964,-5.5643577707173,0.000861906477464646,0.0485474728426847,3.16715262647649,0.922077883334167,1]
["Solyc12g056660","SL3.0ch12",63615516,63617516,"-",199,353,211,523,36.051,28.747,-7.3041306322316,0.0144424711523423,0.686466780257344,3.04060007974051,0.130774361196144,0.570315453702807]
["Solyc12g056880","SL3.0ch12",63901662,63903662,"+",464,26,555,106,94.694,83.964,-10.730186174318,6.94730174864373e-08,0,-3.91085760741443,1,1]
["Solyc12g056990","SL3.0ch12",64019567,64021567,"+",1082,271,1133,349,79.97,76.451,-3.5196938277811,0.0445038467409876,-0.508710851573158,-0.959249616964307,0.659555261986116,1]
["Solyc12g087810","SL3.0ch12",64300984,64302984,"-",194,460,145,501,29.664,22.446,-7.2177881292546,0.0088609335095136,-0.490985699813478,5.13973837806209,0.095683060578163,0.479117650125999]
["Solyc12g087960","SL3.0ch12",64438440,64440440,"+",741,381,754,545,66.043,58.045,-7.9981310181011,0.000246080600923312,-0.521295822004424,5.6203468074792,0.109458469030899,0.516164867540829]
["Solyc12g088110","SL3.0ch12",64567455,64569455,"-",163,612,121,645,21.032,15.796,-5.2359134169965,0.0181774986624296,-2.0589602094265,-3.82761176906435,1,1]
["Solyc12g088120","SL3.0ch12",64565784,64567784,"+",532,178,575,262,74.93,68.698,-6.2318474767362,0.0168599203653295,0,-3.91085760741443,1,1]
["Solyc12g088190","SL3.0ch12",64610799,64612799,"+",350,558,280,759,38.546,26.949,-11.597266093711,4.67191154534993e-07,7.43432869945358,-1.03171731523323,0.000197823023187456,5.96102265658713E-3]
["Solyc12g088250","SL3.0ch12",64689665,64691665,"+",881,431,760,503,67.149,60.174,-6.9752018036807,0.000939174112527838,5.75220682278221,1.08164420914617,0.00239088120020017,0.0391203288054711]
["Solyc12g088260","SL3.0ch12",64694726,64696726,"+",90,215,35,183,29.508,16.055,-13.453150849752,1.31412277996388E-3,0,-3.91085760741443,1,1]
["Solyc12g088270","SL3.0ch12",64699214,64701214,"+",626,298,579,349,67.749,62.392,-5.3566763696074,0.0316590414537731,0,-3.87428074584103,1,1]
["Solyc12g088340","SL3.0ch12",64743541,64745541,"+",195,185,108,248,51.316,30.337,-20.978710821999,7.72905616992912e-08,-0.190037332228862,5.42907414488287,0.482811311867075,1]
["Solyc12g088410","SL3.0ch12",64784704,64786704,"-",662,689,648,1030,49.001,38.617,-10.383338523797,1.08711514564099e-07,1.62069000210431,0.942667951541618,0.0127603836693422,0.124376242549712]
["Solyc12g088500","SL3.0ch12",64820946,64822946,"-",2231,334,2396,456,86.979,84.011,-2.9673373085199,5.43128173645103E-3,0.818269353184725,-1.12495752754471,0.540691371236864,1]
["Solyc12g088540","SL3.0ch12",64864990,64866990,"-",420,118,435,196,78.067,68.938,-9.1287211542427,1.4914842702882E-3,0,-3.91085760741443,1,1]
["Solyc12g088710","SL3.0ch12",64952925,64954925,"-",507,108,501,173,82.439,74.332,-8.1066801765941,0.00146561758761584,1.85979036698304,-3.53908707961408,1,1]
["Solyc12g088720","SL3.0ch12",64955700,64957700,"+",295,232,339,400,55.977,45.873,-10.104428518974,1.37640694497992E-3,0.126242312842339,9.05002545187246,0.625525790973862,1]
["Solyc12g089170","SL3.0ch12",65269689,65271689,"-",743,66,886,133,91.842,86.948,-4.8937917515294,0.00258658344274868,-2.01701254595576,-3.53602734532453,0.999999999999999,1]
["Solyc12g089200","SL3.0ch12",65295608,65297608,"+",175,140,169,256,55.556,39.765,-15.790849673203,1.06195023230544E-4,-0.767925741556339,-2.07141725495362,0.644246149893821,1]
["Solyc12g089360","SL3.0ch12",65468716,65470716,"-",6,46,0,116,11.538,0,-11.538461538461,2.21506122868196E-3,0,-3.91085760741443,1,1]
["Solyc12g095810","SL3.0ch12",65908427,65910427,"+",392,645,429,892,37.801,32.475,-5.3259526220237,0.0169586706500235,0.675879638655302,0.957113734062791,0.307627699776431,0.907108620412481]
["Solyc12g096110","SL3.0ch12",66147680,66149680,"+",101,476,94,625,17.504,13.074,-4.4306192646729,0.0484294119957274,3.59904346295735,-1.79951352637693,0.0814808852785868,0.433677483576055]
["Solyc12g096200","SL3.0ch12",66202568,66204568,"-",61,38,35,49,61.616,41.667,-19.949494949495,0.0168850759688259,0,-3.51490032501125,1,1]
["Solyc12g096370","SL3.0ch12",66302913,66304913,"-",790,307,1104,538,72.015,67.235,-4.7795060607104,0.0186285490938963,0.286747622232617,3.6558873266412,0.413094888296804,1]
["Solyc12g096780","SL3.0ch12",66536373,66538373,"+",768,187,717,238,80.419,75.079,-5.3403141361257,0.0133526037214364,0,-3.75677933962473,1,1]
["Solyc12g097050","SL3.0ch12",66681844,66683844,"+",209,38,229,175,84.615,56.683,-27.932216298553,7.75144180491299e-13,-0.974315317221953,-3.19895789505985,0.642720510024782,1]
["Solyc12g098300","SL3.0ch12",66844208,66846208,"+",500,220,532,340,69.444,61.009,-8.4352701325178,1.62727123946283E-3,0,-3.91085760741443,1,1]
["Solyc12g098530","SL3.0ch12",66989051,66991051,"-",1466,95,1510,148,93.914,91.074,-2.8405749616133,0.00670932752618138,0.627036050500629,4.03379373495084,0.0487008510777942,0.314031375761771]
["Solyc12g098600","SL3.0ch12",67028423,67030423,"+",552,422,476,455,56.674,51.128,-5.5456917447623,0.0314797381046982,-1.06845030377045,4.06796060705703,0.189362946585311,0.707524691681123]
["Solyc12g099040","SL3.0ch12",67322049,67324049,"+",587,270,664,400,68.495,62.406,-6.0887340872601,0.0135837377052866,3.54430203925922,-3.59313229895585,0.428379993830691,1]
["Solyc12g099100","SL3.0ch12",67349092,67351092,"+",3,23,2,198,11.538,1,-10.538461538461,0.0233675229679287,0.292719846433748,6.29903157973647,0.359835920482459,0.977861358746133]
["Solyc12g099220","SL3.0ch12",67421279,67423279,"-",773,389,721,442,66.523,61.995,-4.5283948717114,0.0425099918856063,0,-3.91085760741443,1,1]
["Solyc12g099500","SL3.0ch12",67608122,67610122,"-",188,544,131,692,25.683,15.917,-9.7656846536396,1.39360909616547e-05,0.385727637629595,7.35397338436693,0.324917534979485,0.932866462606054]
["Solyc12g099515","SL3.0ch12",67624521,67626521,"-",543,471,531,621,53.55,46.094,-7.4565458579882,1.82746834195591E-3,1.91240243366122,2.37241961404225,1.43040768376679E-4,0.00473291600675029]
["Solyc12g099650","SL3.0ch12",67688849,67690849,"+",301,363,263,432,45.331,37.842,-7.4895986824998,0.0132867020137646,2.14629792521128,4.37963964894875,0.00360038901018052,0.051614715076608]
["Solyc12g099710","SL3.0ch12",67720254,67722254,"+",38,16,41,126,70.37,24.551,-45.819472166778,3.07671438976169e-08,-0.184830748814143,5.2151773837404,0.555327335432958,1]
["Solyc12g099730","SL3.0ch12",67732711,67734711,"-",288,488,241,669,37.113,26.484,-10.629885578339,2.07282708850329e-05,3.28603618722232,-2.87597208106449,0.493401936046174,1]
["Solyc12g099760","SL3.0ch12",67759715,67761715,"-",15,313,5,397,4.573,1.244,-3.32938963718,0.0210965596080103,-0.422768401312402,5.85725792045328,0.179190627662227,0.685136396226067]
["Solyc12g099870","SL3.0ch12",67816286,67818286,"-",50,138,0,95,26.596,0,-26.595744680851,2.8319323143724e-09,0,-2.7293305007382,1,1]
["Solyc12g100000","SL3.0ch12",67893948,67895948,"+",24,168,8,201,12.5,3.828,-8.6722488038278,0.00421189704746037,-0.221317604896178,5.03909922455397,0.442006548311373,1]
["Solyc12g100170","SL3.0ch12",67973773,67975773,"+",19,129,2,179,12.838,1.105,-11.732865462147,6.32587369580666e-05,6.58475308073962,-0.840707422538963,0.0029491791284651,0.0452925028196392]
["Solyc12g100270","SL3.0ch12",68021914,68023914,"+",122,211,149,423,36.637,26.049,-10.587685587686,2.76177608352926E-3,11.045793695664,2.63727115791274,0.000312550408634253,0.00845635629049166]
["Solyc12g100310","SL3.0ch12",68065572,68067572,"-",546,468,470,495,53.846,48.705,-5.1414906337186,0.0425814378346186,0.294473150773944,5.72997225902678,0.337819756665695,0.951381048783523]

{"sheet":"PHYB1B2_vs_WT_BK_hypermethylate","index":7,"n_rows":9572,"n_cols":17,"rows_kept":4500,"cut":true,"bounds":{"rows_first":2000,"rows_last":500,"rows_between":2000,"halvings":0}}
["Supplementary Table 13. Total differentially methylated promoters (DMPs) in CHG context"]
["ID","chr","from","to","strand","met_WT","unmet_WT","met_PHYB1B2","unmet_PHYB1B2","X.met_WT","X.met_PHYB1B2","X.diff_PHYB1B2.ctrl","FDR_diff_PHYB1B2.WT","logFC_PHYB1B2","logCPM_PHYB1B2","PValue_PHYB1B2","padj_PHYB1B2"]
["Solyc00g005084","SL3.0ch00",807592,809592,"+",622,151,626,106,80.466,85.519,5.0534077011714,0.0193863529338734,0,-3.91085760741443,1,1]
["Solyc00g005850","SL3.0ch00",3432603,3434603,"-",1029,187,1027,134,84.622,88.458,3.8365151412122,0.0150917198256412,0,-3.91085760741443,1,1]
["Solyc00g006805","SL3.0ch00",5780749,5782749,"-",1085,128,765,55,89.448,93.293,3.845032473408,0.00832959003347594,0.216038328688776,-2.36691828856068,0.933881245757083,1]
["Solyc00g006860","SL3.0ch00",6280339,6282339,"-",469,117,403,68,80.034,85.563,5.5285030035579,0.0397149890651751,0,-3.91085760741443,1,1]
["Solyc00g006867","SL3.0ch00",6390079,6392079,"+",42,550,191,527,7.095,26.602,19.507076714598,7.96229029644077e-20,1.81735752678876,-0.558251759538668,0.0436852225871048,0.292423539929366]
["Solyc00g006890","SL3.0ch00",6446980,6448980,"+",476,75,393,33,86.388,92.254,5.8651363717696,0.00937853505048562,0,-3.91085760741443,1,1]
["Solyc00g007550","SL3.0ch00",6650039,6652039,"-",240,341,359,328,41.308,52.256,10.948096816461,4.84065982577587E-4,3.85241885635068,-3.43052628147651,0.267023879796986,0.847591022855933]
["Solyc00g007950","SL3.0ch00",6926603,6928603,"-",88,10,50,0,89.796,100,10.204081632653,0.0310464099710167,0,-3.91085760741443,1,1]
["Solyc00g008020","SL3.0ch00",6991194,6993194,"-",3,9,30,1,25,96.774,71.774193548387,2.14056822277404e-05,0,-3.91085760741443,1,1]
["Solyc00g008040","SL3.0ch00",7005181,7007181,"-",153,84,310,79,64.557,79.692,15.134554684195,0.000162330228557291,0,-3.91085760741443,1,1]
["Solyc00g008110","SL3.0ch00",7099931,7101931,"-",94,27,310,38,77.686,89.08,11.394509356892,0.00825925527282191,0,-3.91085760741443,1,1]
["Solyc00g008800","SL3.0ch00",7659775,7661775,"-",443,92,341,35,82.804,90.691,7.8877510439451,0.00204963934428506,0,-3.91085760741443,1,1]
["Solyc00g009020","SL3.0ch00",7793998,7795998,"+",1075,302,1244,165,78.068,88.29,10.221302726069,8.30294854377416e-12,0.190117269525115,7.62400916820391,0.459075707578805,1]
["Solyc00g009050","SL3.0ch00",7822149,7824149,"-",1807,570,2474,266,76.02,90.292,14.271777281674,1.73453307132784e-41,5.87051709319639,-1.83143939226503,0.00260560370971653,0.0416803369808322]
["Solyc00g009110","SL3.0ch00",7871111,7873111,"+",44,893,282,1167,4.696,19.462,14.765859942418,7.52475877212749e-26,1.47506682181694,3.27195840491963,0.022500245987099,0.186250700298369]
["Solyc00g009141","SL3.0ch00",7897016,7899016,"-",545,111,580,65,83.079,89.922,6.8432123274721,0.0011874208212232,0.322742271561578,4.45932488007655,0.277519591143608,0.865847316386881]
["Solyc00g010930","SL3.0ch00",9019959,9021959,"+",772,210,667,133,78.615,83.375,4.7599287169043,0.0226681813278885,0,-3.91085760741443,1,1]
["Solyc00g011890","SL3.0ch00",9403098,9405098,"-",443,569,647,606,43.775,51.636,7.8613698664707,0.000739058353186751,-0.320787952594974,7.36530330208955,0.330645478883871,0.941011149955126]
["Solyc00g012706","SL3.0ch00",9705530,9707530,"-",760,337,784,257,69.28,75.312,6.0323456602016,0.00531500037034521,0,-3.91085760741443,1,1]
["Solyc00g017540","SL3.0ch00",10558570,10560570,"+",167,106,181,75,61.172,70.703,9.5309638278388,0.0392783846763187,0,-3.91085760741443,1,1]
["Solyc00g020545","SL3.0ch00",10945268,10947268,"+",6692,3674,3948,1688,64.557,70.05,5.4924743733506,3.16353349571939e-11,-2.57331702043306,-3.07629557896507,0.198185763578075,0.725039213630009]
["Solyc00g022090","SL3.0ch00",11058576,11060576,"-",86,7400,307,19187,1.149,1.575,0.42603242752293,0.0188313909654731,-2.02658284136228,-3.7903905899943,0.999999999999999,1]
["Solyc00g022107","SL3.0ch00",11072272,11074272,"-",595,422,699,332,58.505,67.798,9.2928460592813,6.96627799350894e-05,-0.0552234248720084,-2.03864792398076,1,1]
["Solyc00g024160","SL3.0ch00",11230391,11232391,"-",719,365,710,275,66.328,72.081,5.7528049899788,0.0115239471579523,3.65209184002688,-3.38126235307709,0.340695365285218,0.954117743933737]
["Solyc00g024570","SL3.0ch00",11259566,11261566,"+",3850,959,4256,869,80.058,83.044,2.9856782759967,0.000497545036120462,0,-3.7595815468704,1,1]
["Solyc00g026165","SL3.0ch00",11408797,11410797,"+",22,16,44,10,57.895,81.481,23.586744639376,0.0342210825551158,0,-3.87282557379725,1,1]
["Solyc00g026907","SL3.0ch00",11445381,11447381,"-",57,289,117,276,16.474,29.771,13.297003927106,9.89508555885489e-05,0,-3.91085760741443,1,1]
["Solyc00g028760","SL3.0ch00",11537778,11539778,"+",1686,287,2066,238,85.454,89.67,4.2165149659289,1.45061686828429E-4,0,-3.91085760741443,1,1]
["Solyc00g030510","SL3.0ch00",11649548,11651548,"+",168,232,208,210,42,49.761,7.7607655502392,0.04970670752004,0,-3.91085760741443,1,1]
["Solyc00g030520","SL3.0ch00",11657277,11659277,"-",841,191,892,124,81.492,87.795,6.3030275285357,0.000352673800288279,-0.215082378377368,3.52117013121424,0.585932642509375,1]
["Solyc00g031500","SL3.0ch00",11714108,11716108,"-",382,53,217,12,87.816,94.76,6.9437333734879,0.00913992715121635,0,-3.91085760741443,1,1]
["Solyc00g040390","SL3.0ch00",12201979,12203979,"+",93,160,242,129,36.759,65.229,28.470217231497,4.5856367736132e-11,0,-3.91085760741443,1,1]
["Solyc00g042850","SL3.0ch00",12333955,12335955,"+",37,426,74,454,7.991,14.015,6.0237908240068,0.00812906120237197,0,-3.87150960665568,1,1]
["Solyc00g042854","SL3.0ch00",12376717,12378717,"+",534,400,626,357,57.173,63.683,6.5091567351616,0.00914367733641416,0,-3.91085760741443,1,1]
["Solyc00g042858","SL3.0ch00",12406911,12408911,"-",595,232,666,184,71.947,78.353,6.406145529554,0.00691824030976757,0,-3.91085760741443,1,1]
["Solyc00g044755","SL3.0ch00",12523754,12525754,"-",146,280,300,332,34.272,47.468,13.196053960896,0.000102655095767161,0,-3.91085760741443,1,1]
["Solyc00g046580","SL3.0ch00",12523754,12525754,"-",146,280,300,332,34.272,47.468,13.196053960896,0.000102655095767161,0,-3.91085760741443,1,1]
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["Solyc12g100150","SL3.0ch12",67963908,67965908,"+",33,213,61,229,13.415,21.034,7.6198486122792,0.0400701501162462,-0.935129276433561,-2.47412922827029,0.684556424741081,1]
["Solyc12g100180","SL3.0ch12",67977198,67979198,"+",78,377,137,455,17.143,23.142,5.9990347490347,0.036935104138054,1.85494019766793,-3.48457333746722,1,1]
["Solyc12g100340","SL3.0ch12",68086246,68088246,"-",710,189,866,164,78.977,84.078,5.1010291910105,0.0107549798435961,0,-3.91085760741443,1,1]
["Solyc12g100350","SL3.0ch12",68089938,68091938,"+",892,344,1025,256,72.168,80.016,7.8473280128541,2.56222106405486e-05,2.06140478620785,-0.782669363899267,0.0642736811343032,0.376135639203494]
["Solyc12g100353","SL3.0ch12",68098699,68100699,"+",6,639,26,631,0.93,3.957,3.0271494814343,1.53958583394913E-3,0,-3.91085760741443,1,1]