{"text_format":"3","workbook":"xls","n_sheets":2,"sheets":["Annotation","Classification"],"read":"whole","date_system":"1900","formulas":"cached_only"}

{"sheet":"Annotation","index":0,"n_rows":146,"n_cols":13,"rows_kept":146,"flags":["formulas_cached_only"]}
["Table S5. Major discordances annotated in the current build of rice pseudomolecules"]
["CHROMOSOME","CLONENAME","ACCESSION","VERSION","LABORATORY","direction","clone size","start @MTP","end @MTP","length @MTP","Discordance Class","Clone Phase","Comments"]
[1,"physical gap 02",{"$nulls":5},10053432,10054431,1000,1,"NA","A 12 kb gap."]
[1,"physical gap 03",{"$nulls":5},11494794,11495793,1000,1,"NA","A 13 kb gap."]
[1,"physical gap 04",{"$nulls":5},14990749,14991748,1000,1,"NA","An 18 kb gap."]
[1,"physical gap 05",{"$nulls":5},16847169,16848168,1000,1,"NA","A 595 kb gap."]
[1,"P0507H06","AP003144","AP003144.1","RGP","+",136351,17411461,17486824,75364,3,"PLN"]
[1,"physical gap 06",{"$nulls":5},25477666,25478665,1000,1,"NA","A 3 kb gap."]
[1,"B1131B07","AP003408","AP003408.3","RGP","+",109135,29688356,29786122,97767,3,"PLN"]
[1,"OJ1529_G03","AP003446","AP003446.3","RGP","+",100635,34908551,34977989,69439,2,"PLN"]
[1,"physical gap 07",{"$nulls":5},40297655,40298654,1000,1,"NA","An 8 kb gap."]
[1,"P0504E02","AP003269","AP003269.2","RGP","+",137468,41112928,41248031,135104,2,"PLN"]
[2,"OSJNBa0064G16","AP005649","AP005649.3","RGP","+",166453,2385008,2550532,165525,5,"PLN"]
[2,"physical gap 01",{"$nulls":5},5969519,5970518,1000,1,"NA","A 13 kb gap."]
[2,"P0693E08","AP005428","AP005428.2","RGP","+",157969,9539327,9694651,155325,4,"PLN"]
[2,"P0572A04","AP005009","AP005009.3","RGP","+",132018,11835177,11935145,99969,3,"PLN"]
[2,"physical gap 02",{"$nulls":5},13681860,13682859,1000,1,"NA","A 460 kb gap."]
[2,"OJ1471_E11","AP004062","AP004062.3","RGP","+",103912,18487749,18577770,90022,3,"PLN"]
[2,"physical gap 03",{"$nulls":5},18795363,18796362,1000,1,"NA","An 8 kb gap."]
[2,"OJ1791_B03","AP005385","AP005385.3","RGP","+",166214,23416036,23581135,165100,5,"PLN"]
[2,"physical gap 04",{"$nulls":5},24815506,24816505,1000,1,"NA"]
[3,"physical gap 02",{"$nulls":5},4867170,4868169,1000,1,"NA","A 35 kb gap."]
[3,"OSJNBb0078O24","AC126224","AC126224.3","AGI","+",135980,13345390,13464658,119269,4,"PLN"]
[3,"physical gap 03",{"$nulls":5},13464659,13465658,1000,1,"NA","A 256 kb gap."]
[3,"OSJNBb0033D20","AC137076","AC137076.1","CSHL","+",128707,13782254,13899818,117565,2,"PLN"]
[3,"physical gap 04",{"$nulls":5},16362795,16363794,1000,1,"NA","A 4 kb gap. The gap is not obvious in the graph."]
[3,"physical gap 05",{"$nulls":5},16386790,16387789,1000,1,"NA","A 85 kb gap."]
[3,"OJ1212_C05","AC092262","AC092262.6","TIGR","+",113266,16966119,17044740,78622,3,"PLN"]
[3,"OJ1324_A07","AC115688","AC115688.8","TIGR","-",114629,18965890,19055317,89428,2,"PLN"]
[3,"physical gap 06",{"$nulls":5},19544601,19545600,1000,1,"NA","A 342 kb gap."]
[3,"physical gap 07",{"$nulls":5},31112024,31113023,1000,1,"NA","A 100 kb gap."]
[3,"physical gap 08",{"$nulls":5},31123481,31124480,1000,1,"NA","A 9 kb gap. The gap is not obvious in the graph."]
[4,"physical gap 02",{"$nulls":5},932184,933183,1000,1,"NA","An 81 kb gap."]
[4,"OSJNBb0016B03","AL731635","AL731635.3","NCGR","+",125780,2351242,2413333,62092,2,"PLN"]
[4,"OSJNBa0056L23","AL731603","AL731603.3","NCGR","+",175593,2535550,2709367,173818,5,"PLN"]
[4,"OSJNBa0057M08","AL731640","AL731640.5","NCGR","+",178366,3274041,3433956,159916,5,"HTG"]
[4,"physical gap 03",{"$nulls":5},8427677,8428676,1000,1,"NA","A 34 kb gap."]
[4,"OSJNBa0061C08","BX569685","BX569685.1","NCGR","+",145980,9124431,9230105,105675,3,"PLN"]
[4,"physical gap 04",{"$nulls":5},9349011,9350010,1000,1,"NA","A 34 kb gap."]
[4,"OSJNBb0062N22","BX890594","BX890594.1","NCGR","+",181586,9744497,9888198,143702,3,"PLN"]
[4,"OSJNBa0042D13","AL731604","AL731604.3","NCGR","+",163429,10476914,10611640,134727,3,"PLN"]
[4,"OSJNBa0072D08","AL731611","AL731611.2","NCGR","+",142814,10967250,11081707,114458,5,"PLN","There could be misassemblies on AL731611."]
[4,"OSJNBa0009K15","AL731585","AL731585.5","NCGR","+",185021,11629449,11809780,180332,3,"PLN"]
[4,"OSJNBa0094P09","AL731625","AL731625.2","NCGR","+",145462,11936726,12019569,82844,5,"HTG"]
[4,"OSJNBa0004L19","AL731586","AL731586.4","NCGR","+",153401,14381653,14488922,107270,5,"HTG"]
[4,"OSJNBa0082E08","AL731608","AL731608.3","NCGR","+",156779,15184800,15268475,83676,5,"HTG"]
[4,"physical gap 05",{"$nulls":5},15655633,15656632,1000,1,"NA","A 63 kb gap."]
[4,"OSJNBa0091C07","AL731624","AL731624.3","NCGR","+",138383,16777717,16877829,100113,4,"PLN"]
[4,"OSJNBb0066J23","AL606990","AL606990.3","NCGR","+",156934,16966642,17091555,124914,4,"PLN"]
[4,"OSJNBa0072K14","AL606621","AL606621.3","NCGR","+",139855,19353025,19477789,124765,3,"PLN"]
[4,"OSJNBa0042I15","AL731641","AL731641.4","NCGR","+",158354,20133987,20260425,126439,5,"HTG"]
[4,"OSJNBa0028I23","AL662944","AL662944.3","NCGR","+",148736,20769637,20893169,123533,5,"PLN"]
[4,"physical gap 06",{"$nulls":5},22047023,22048022,1000,1,"NA","A 25 kb gap."]
[4,"physical gap 07",{"$nulls":5},22098902,22099901,1000,1,"NA","A 64 kb gap."]
[4,"physical gap 08",{"$nulls":5},22273506,22274505,1000,1,"NA","A 5 kb gap."]
[4,"OSJNBa0070O11","AL606445","AL606445.2","NCGR","+",134231,32846467,32957579,111113,3,"PLN"]
[5,"P0519E07","AC087552","AC087552.3","ASPGC","+",151399,1997268,2093560,96293,3,"PLN"]
[5,"physical gap 01",{"$nulls":5},7361120,7362119,1000,1,"NA","A 9 kb gap."]
[5,"P0690B12","AC136229","AC136229.3","ASPGC","+",135323,11531670,11666203,134534,2,"PLN"]
[5,"OSJNBa0050A24","AC144453","AC144453.2","ASPGC","+",142574,12197256,12289258,92003,4,"PLN"]
[5,"P0697B04","P0697B04",null,"ASPGC","+",147577,12427597,12575173,147577,3,"HTG"]
[5,"OSJNBa0082F22","AC135915","AC135915.2","ASPGC","+",176038,13199079,13346732,147654,2,"PLN"]
[5,"OSJNBb0020D14","AC134343","AC134343.2","ASPGC","+",120440,15376347,15429414,53068,5,"HTG"]
[5,"physical gap 02",{"$nulls":5},17142001,17143000,1000,1,"NA","A 2 kb gap."]
[5,"physical gap 03",{"$nulls":5},21551073,21552072,1000,1,"NA","A 5 kb gap."]
[5,"P0015C02","AC135423","AC135423.2","ASPGC","+",147407,23203577,23213380,9804,4,"PLN"]
[5,"B1155G07","AC130604","AC130604.4","ASPGC","+",146712,25420440,25484193,63754,4,"PLN"]
[5,"physical gap 04",{"$nulls":5},27174275,27175274,1000,1,"NA","A 44 kb gap."]
[5,"OJ1263_E10","AC093956","AC093956.2","ASPGC","+",116469,27537127,27624342,87216,2,"PLN"]
[5,"OSJNBa0001A14","AC144735","AC144735.2","ASPGC","+",129292,27768802,27882346,113545,2,"PLN"]
[5,"P0663C08","AC130728","AC130728.2","ASPGC","+",142196,29479725,29583868,104144,3,"PLN"]
[5,"OSJNBa0035I01","AC137000","AC137000.2","ASPGC","+",147813,29770691,29883640,112950,3,"PLN"]
[6,"physical gap 02",{"$nulls":5},10579631,10580630,1000,1,"NA","A 2 kb gap."]
[6,"physical gap 03",{"$nulls":5},15423584,15424583,1000,1,"NA","An 815 kb gap."]
[6,"OSJNBa0061G23","AP006553","AP006553.3","RGP","+",144220,18389762,18481995,92234,5,"PLN"]
[6,"OSJNBa0049C15d","AP007274","AP007274.1","RGP","+",93841,22857085,22918170,61086,5,"HTG"]
[6,"P0481H08","AP003629","AP003629.3","RGP","+",146841,23903186,24049532,146347,3,"PLN"]
[7,"OSJNBa0024L18","AP005409","AP005409.4","RGP","+",150128,2939697,3071922,132226,5,"PLN","This location is puzzling. There may be problems with both OM and pseudomolecule. There is a segmental duplication, and there should be a 30 kb physical gap."]
[7,"OSJNBa0081K20","AP005171","AP005171.3","RGP","+",117287,5473190,5572051,98862,5,"PLN"]
[7,"B1100H02","AP006447","AP006447.4","RGP","+",128773,9432872,9514636,81765,2,"PLN"]
[7,"physical gap 02",{"$nulls":5},11609591,11610590,1000,1,"NA","A 23 kb gap."]
[7,"physical gap 03",{"$nulls":5},12185871,12186870,1000,1,"NA","A 60 kb gap."]
[7,"OJ1047_A06","AP003802","AP003802.2","RGP","+",111673,15407535,15458260,50726,4,"PLN"]
[7,"P0683C09","AP004348","AP004348.4","RGP","+",185139,17875568,18011733,136166,2,"PLN"]
[7,"OJ1060_D03","AP003803","AP003803.5","RGP","+",102178,23724933,23811150,86218,2,"PLN"]
[7,"P0519E12","AP004339","AP004339.3","RGP","+",152448,26168017,26314176,146160,4,"PLN"]
[7,"OSJNBa0030A22","AP006456","AP006456.4","RGP","+",141096,27332299,27402814,70516,2,"PLN"]
[7,"P0304A10","AP006269","AP006269.3","RGP","+",21211,28485272,28493010,7739,3,"PLN"]
[8,"OJ1177_E11","AP003905","AP003905.3","RGP","+",92375,3162203,3242642,80440,4,"PLN"]
[8,"P0438H08","AP004460","AP004460.2","RGP","+",148626,3242643,3377406,134764,2,"PLN"]
[8,"OSJNBa0002E10","AP006857","AP006857.2","RGP","+",140486,6826052,6896114,70063,4,"PLN"]
[8,"physical gap 02",{"$nulls":5},11171230,11172229,1000,1,"NA","A 24 kb gap."]
[8,"OSJNBa0049I01","AP005490","AP005490.3","RGP","+",140261,14496071,14552640,56570,3,"PLN"]
[8,"P0475C12","AP004375","AP004375.3","RGP","+",140863,15969065,16076071,107007,4,"PLN"]
[8,"B1104G07","AP005096","AP005096.2","RGP","+",119643,16220248,16336712,116465,2,"PLN"]
[8,"OJ1770_H03","AP005298","AP005298.3","RGP","+",189893,17237809,17336515,98707,2,"PLN"]
[8,"P0026F07","AP000364","AP000364.1","RGP","+",137354,24553496,24636341,82846,2,"PLN"]
[8,"P0702C09","AP005528","AP005528.2","RGP","+",138203,26649329,26733923,84595,4,"PLN"]
[8,"P0543D10","AP004587","AP004587.3","RGP","+",134866,28168802,28258640,89839,3,"PLN"]
[9,"physical gap 02",{"$nulls":5},2787792,2788791,1000,1,"NA","A 301 kb gap."]
[9,"physical gap 03",{"$nulls":5},11419063,11420062,1000,1,"NA","A 17 kb gap."]
[9,"physical gap 04",{"$nulls":5},13605665,13606664,1000,1,"NA","An 8 kb gap"]
[9,"OSJNBa0087J09","AC108761","AC108761.2","KRGRP","+",153351,18538605,18679995,141391,5,"PLN"]
[9,"OSJNBa0046G16","AC108756","AC108756.1","KRGRP","-",154082,18679996,18771125,91130,4,"HTG"]
[9,"physical gap 05",{"$nulls":5},20279472,20280471,1000,1,"NA","A 9 kb gap."]
[9,"physical gap 06",{"$nulls":5},20406895,20407894,1000,1,"NA","A 13 kb gap."]
[10,"OSJNBa0065H03","AC037197","AC037197.2","AGI","+",141017,430663,557811,127149,4,"PLN"]
[10,"OSJNBb0016M10","AC091665","AC091665.3","AGI","+",118101,2841029,2958037,117009,3,"PLN"]
[10,"physical gap 02",{"$nulls":5},4094890,4095889,1000,1,"NA","A 54 kb gap."]
[10,"physical gap 03",{"$nulls":5},4225483,4226482,1000,1,"NA","A 56 kb gap."]
[10,"OSJNBa0011A24","AC113336","AC113336.2","CSHL","+",176832,5059064,5220783,161720,5,"PLN"]
[10,"OSJNBa0047G15","AC083944","AC083944.8","CSHL","+",166474,5350612,5510404,159793,5,"PLN"]
[10,"OSJNBa0079H13","AC104616","AC104616.5","TIGR","+",116863,6131030,6134299,3270,5,"PLN"]
[10,"physical gap 04",{"$nulls":5},7173950,7174949,1000,1,"NA","A 15 kb gap."]
[10,"physical gap 05",{"$nulls":5},7744026,7745025,1000,1,"NA","A 59 kb gap."]
[10,"physical gap 06",{"$nulls":5},7945631,7946630,1000,1,"NA","A 0.6 kb gap. The gap is not clearly seen in the graph."]
[10,"physical gap 07",{"$nulls":5},8170394,8171393,1000,1,"NA","A 395 kb gap."]
[10,"physical gap 08",{"$nulls":5},9881733,9882732,1000,1,"NA","A 34 kb gap."]
[10,"OSJNBa0035F15","AC119148","AC119148.2","CSHL","+",138335,10028150,10166478,138329,2,"PLN"]
[10,"physical gap 09",{"$nulls":5},12198461,12199460,1000,1,"NA","A 52 kb gap."]
[10,"B1288B10","AC146481","AC146481.2","TIGR","+",58734,18577138,18602706,25569,3,"PLN"]
[10,"OSJNBa0015J15","AC026758","AC026758.8","TIGR","-",144798,21584481,21725795,141315,3,"PLN"]
[10,"OSJNBa0010C11","AC069300","AC069300.7","TIGR","+",147117,21854449,21992194,137746,3,"PLN"]
[11,"OSJNBa0018J01","AC146328","AC146328.3","TIGR","-",82510,4178094,4240413,62320,2,"PLN"]
[11,"OSJNBa0044D15","AC119071","AC119071.1","GCOW","+",144544,6757439,6803742,46304,4,"PLN"]
[11,"physical gap 02",{"$nulls":5},7313364,7314363,1000,1,"NA","A 32 kb gap."]
[11,"physical gap 03",{"$nulls":5},8924808,8925807,1000,1,"NA","A 36 kb gap."]
[11,"OSJNBa0072N24","AC133006","AC133006.6","TIGR","+",163337,10023611,10170571,146961,5,"PLN"]
[11,"OSJNBa0038F10","AC120306","AC120306.3","TIGR","-",68992,11278833,11327843,49011,4,"PLN"]
[11,"physical gap 04",{"$nulls":5},12179037,12180036,1000,"1,5","HTG_phase1, and NA","A 2,426 kb gap."]
[11,"physical gap 05",{"$nulls":5},13410597,13411596,1000,1,"NA","A 63 kb gap."]
[11,"OSJNBb0091D07","AC132003","AC132003.4","IIRGS","+",144652,15835559,15980210,144652,3,"PLN"]
[11,"OSJNBa0094M06","AC136843","AC136843.6","IIRGS","+",135583,16472883,16546615,73733,5,"PLN"]
[11,"OSJNBa0062E06","AC136491","AC136491.4","IIRGS","+",158842,18311215,18439674,128460,2,"PLN"]
[11,"OSJNOa0281D22","AC151106","AC151106.2","IIRGS","-",35282,19782167,19817448,35282,5,"PLN"]
[11,"OSJNBa0029P13","AC129224","AC129224.2","IIRGS","+",158506,26142184,26299743,157560,5,"PLN"]
[11,"OSJNBb0099J16","AC129227","AC129227.2","IIRGS","-",133198,26769584,26873243,103660,3,"PLN"]
[11,"OSJNBa0030J08","AC145319","AC145319.5","TIGR","+",139725,28597117,28672585,75469,2,"HTG"]
[12,"physical gap 02",{"$nulls":5},12010078,12011077,1000,1,"NA","A 225 kb gap."]
[12,"OSJNBa0080D17","AL954854","AL954854.3","Genoscope","-",159718,15620609,15780326,159718,2,"PLN","Missing two fragments."]
[12,"physical gap 03",{"$nulls":5},16625441,16626440,1000,1,"NA","A 61 kb gap."]
[12,"OSJNBa0061G08","AL772413","AL772413.6","Genoscope","+",150594,17106900,17207693,100794,4,"HTG"]
[12,"physical gap 04",{"$nulls":5},20552488,20553487,1000,1,"NA","A 183 kb gap."]
[12,"OSJNBa0055K18","AL731736","AL731736.6","Genoscope","+",131175,21325441,21454134,128694,2,"HTG","Missing fragment at two locations."]
[12,"OJ1057_A02","AL772422","AL772422.6","Genoscope","-",92517,23722025,23794830,72806,2,"HTG"]
[12,"OSJNBb0003F09","AC027133","AC027133.3","PGIR","+",159600,26904895,27001124,96230,4,"PLN"]

{"sheet":"Classification","index":1,"n_rows":6,"n_cols":2,"rows_kept":6,"merged":[[0,0,0,1]],"flags":["formulas_cached_only"]}
["Pseudomolecule and Optical Map discordance classification:"]
["Class 1","Physical gaps in the pseudomolecule."]
["Class 2","Missed fragment(s) or extra fragment(s). This means an extra fragment(s) either on the optical map or the pseudomolecule; Only when the size difference is larger than 5 kb the location is annotated."]
["Class 3","Significant size difference (mostly > 5 kb). The number of fragments are usually the same."]
["Class 4","Multiple different SwaI sites in the same area"]
["Class 5","Multiple different SwaI sites and multiple un-matched SwaI fragments. The total sizes are not comparable. There are possible misassemblies."]