Supplementary Table 2. Haplotype tracking variants,,,,,,,,,,,,,,,,,,
CHROM,POS,REF,ALT,AC,AF,MAC,MAF,AF_F1,AF_F2,AF_F3,AF_F4,AF_F5,AF_S1,AF_S2,AF_S3,AF_S4,AF_S5,AF_WT
2L,2348815,T,C,2169,0.95,115,0.05,1,1,1,1,1,1,1,1,1,1,0.837
2L,2348824,T,A,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2348869,T,A,393,0.172,393,0.172,0.001,0,1,1,0.995,0,0,0,0,0,0.137
2L,2348877,G,T,77,0.034,77,0.034,0,0,0,0,0,0,0,0,0,0,0.115
2L,2348929,A,G,109,0.048,109,0.048,0,0,1,1,0,0,0,0,0,0,0.019
2L,2349057,A,T,2169,0.95,115,0.05,1,1,1,1,1,1,1,1,1,1,0.839
2L,2349116,A,G,81,0.035,81,0.035,0,0,0,0,0,0,0,0,1,1,0
2L,2349240,A,T,111,0.049,111,0.049,0,0,0,0,0,0,0,0,0,0,0.166
2L,2349518,T,C,109,0.048,109,0.048,0,0,0,0,0,0,0,0,0,0,0.163
2L,2349594,T,C,101,0.044,101,0.044,0,0,0,0,0,0,1,0,0,0,0.003
2L,2350298,T,A,116,0.051,116,0.051,0,0,0,0,0,0,1,0,0,0,0.025
2L,2350327,C,T,2006,0.878,278,0.122,0.999,1,1,1,1,1,1,1,1,1,0.599
2L,2350334,G,A,91,0.04,91,0.04,0,0,0,0,0,0,0,0,0,0,0.136
2L,2350378,T,C,89,0.039,89,0.039,0,0,0,0,0,0,0,0,0,0,0.133
2L,2351728,A,T,2220,0.972,64,0.028,1,1,1,1,1,1,1,1,1,1,0.906
2L,2351888,C,T,861,0.377,861,0.377,1,0,0,0,0,0,0,0,0,0,0.088
2L,2352060,T,G,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2352097,A,G,852,0.373,852,0.373,1,0,0,0,0,0,0,0,0,0,0.075
2L,2352125,G,A,1993,0.873,291,0.127,1,1,1,1,1,1,1,1,1,1,0.575
2L,2352169,G,A,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2352179,C,G,2220,0.972,64,0.028,1,1,1,1,1,1,1,1,1,1,0.906
2L,2352250,A,C,2220,0.972,64,0.028,1,1,1,1,1,1,1,1,1,1,0.906
2L,2352262,G,A,1994,0.873,290,0.127,1,1,1,1,1,1,1,1,1,1,0.576
2L,2352286,C,T,90,0.039,90,0.039,0,0,0,0,0,0,0,0,0,0,0.128
2L,2352296,C,A,2220,0.972,64,0.028,1,1,1,1,1,1,1,1,1,1,0.906
2L,2352402,G,T,81,0.035,81,0.035,0,0,0,0,0,0,0,0,0,0,0.119
2L,2352455,A,T,219,0.096,219,0.096,0,0,0,0,0.995,0,0,0,0,0,0.027
2L,2352457,G,A,853,0.373,853,0.373,0.999,0,0,0,0,0,0,0,0,0,0.078
2L,2352589,A,C,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2352607,T,A,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2352680,A,G,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2352697,T,A,2104,0.921,180,0.079,1,1,1,1,1,1,1,1,1,1,0.742
2L,2352719,A,T,2104,0.921,180,0.079,1,1,1,1,1,1,1,1,1,1,0.742
2L,2352843,C,T,133,0.058,133,0.058,0,0,0,0,0,1,0,0,0,0,0.018
2L,2352993,T,C,28,0.012,28,0.012,0,0,0,0,0,0,0,0,0,0,0.042
2L,2353036,A,G,1994,0.873,290,0.127,1,1,1,1,1,1,1,1,1,1,0.579
2L,2353037,A,G,179,0.078,179,0.078,0,0,0,0,0,0,0,1,0,0,0
2L,2353070,T,G,111,0.049,111,0.049,0,0,0,0,0,0,0,0,0,0,0.166
2L,2353212,G,A,26,0.011,26,0.011,0,0,0,0,0,0,0,0.147,0,0,0
2L,2353223,T,G,111,0.049,111,0.049,0,0,0,0,0,0,0,0,0,0,0.166
2L,2353299,A,T,109,0.048,109,0.048,0,0,0,0,0,0,0,0,0,0,0.163
2L,2353319,C,T,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2353507,C,T,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2353514,C,T,216,0.095,216,0.095,0,0,0,0,0.984,0,0,0,0,0,0.024
2L,2353650,T,C,394,0.173,394,0.173,0,0,1,1,0.989,0,0,0,0,0,0.142
2L,2354090,A,T,113,0.049,113,0.049,0,0,0,0,0,0,1,0,0,0,0.021
2L,2354502,T,C,108,0.047,108,0.047,0,0,0,0,0,0,0,0,0,0,0.161
2L,2354508,A,C,193,0.085,193,0.085,0,0,0,0,0,1,0,0,0,0,0.107
2L,2354536,A,G,110,0.048,110,0.048,0,0,1,1,0,0,0,0,0,0,0.021
2L,2354539,T,G,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2354587,A,C,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2356487,C,T,2211,0.968,73,0.032,0.999,1,1,1,1,1,1,1,1,1,0.894
2L,2357178,G,T,92,0.04,92,0.04,0,0,0,0,0,0,0,0,0,0,0.13
2L,2357218,C,T,109,0.048,109,0.048,0,0,0,0,0,0,0,0,0,0,0.163
2L,2357446,G,A,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2357532,A,C,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2357537,C,T,193,0.085,193,0.085,0,0,0,0,0,1,0,0,0,0,0.107
2L,2357556,G,A,806,0.353,806,0.353,1,0,0,0,0,0,0,0,0,0,0.016
2L,2357816,A,C,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2357825,C,T,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2357828,C,A,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2357837,A,T,71,0.031,71,0.031,0,0,0,0,0,0,0,0,0,0,0.106
2L,2357850,A,G,81,0.035,81,0.035,0,0,0,0,0,0,0,0,1,1,0
2L,2357859,C,A,193,0.085,193,0.085,0,0,0,0,0,1,0,0,0,0,0.107
2L,2357860,T,A,76,0.033,76,0.033,0,0,0,0,0,0,0,0,0,0,0.113
2L,2357873,A,G,193,0.085,193,0.085,0,0,0,0,0,1,0,0,0,0,0.107
2L,2357955,A,C,870,0.381,870,0.381,1,0,0,0,0,0,0,0,0,0,0.106
2L,2357997,G,A,853,0.373,853,0.373,0.999,0,0,0,0,0,0,0,0,0,0.082
2L,2358316,T,G,81,0.035,81,0.035,0,0,0,0,0,0,0,0,1,1,0
2L,2358667,T,A,800,0.35,800,0.35,0.99,0,0,0,0,0,0,0,0,0,0.019
2L,2358808,G,C,46,0.02,46,0.02,0,0,0,1,0,0,0,0,0,0,0.009
2L,2358818,T,C,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2358884,T,G,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2359201,T,C,2193,0.96,91,0.04,1,1,1,1,1,1,1,1,1,1,0.869
2L,2359245,T,G,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2359297,T,A,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2359337,G,A,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2359353,T,A,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2359458,A,T,109,0.048,109,0.048,0,0,0,0,0,0,0,0,0,0,0.163
2L,2359542,T,A,190,0.083,190,0.083,0,0,0,0,0.005,0.991,0,0.006,0,0,0.1
2L,2360118,A,T,74,0.032,74,0.032,0,0,0,0,0,0,0,0,0,0,0.106
2L,2360133,C,T,2210,0.968,74,0.032,0.999,1,1,1,1,1,1,1,1,1,0.893
2L,2360173,T,A,74,0.032,74,0.032,0,0,0,0,0,0,0,0,0,0,0.11
2L,2360255,C,G,81,0.035,81,0.035,0,0,0,0,0,0,0,0,1,1,0
2L,2360303,C,G,111,0.049,111,0.049,0,0,0,0,0,0,0,0,0,0,0.164
2L,2360508,A,G,2211,0.968,73,0.032,1,1,1,1,1,1,1,1,1,1,0.893
2L,2360595,A,G,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2360605,A,T,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2360682,T,C,40,0.018,40,0.018,0,0,0,0,0,0,0,0,0,0,0.06
2L,2360741,C,T,26,0.011,26,0.011,0,0,0,0,0,0,0,0,0,0,0.025
2L,2361040,A,G,2211,0.968,73,0.032,1,1,1,1,1,1,1,1,1,1,0.894
2L,2361041,T,A,2102,0.92,182,0.08,1,1,1,1,1,1,1,1,1,1,0.751
2L,2361238,C,A,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2361318,A,G,1992,0.872,292,0.128,1,1,1,1,1,1,1,1,1,1,0.585
2L,2361321,T,C,2202,0.964,82,0.036,1,1,1,1,1,1,1,1,1,1,0.882
2L,2361396,C,T,1992,0.872,292,0.128,1,1,1,1,1,1,1,1,1,1,0.584
2L,2361453,A,G,841,0.368,841,0.368,1,0,0,0,0,0,0,0,0,0,0.066
2L,2361850,C,T,111,0.049,111,0.049,0,0,0,0,0,0,0,0,0,0,0.164
2L,2362168,T,A,2192,0.96,92,0.04,1,1,1,1,1,1,1,1,1,1,0.878
2L,2362259,C,G,850,0.372,850,0.372,0.999,0,0,0,0,0,0,0,0,0,0.082
2L,2362368,C,T,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2362375,T,A,139,0.061,139,0.061,0,0,0,0,0,0,0,0,1,1,0.084
2L,2362380,A,C,868,0.38,868,0.38,1,0,0,0,0,0,0,0,0,0,0.106
2L,2362387,G,A,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2362433,A,T,82,0.036,82,0.036,0,0,0,0,0,0,0,0,0,0,0.119
2L,2362436,C,T,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2362455,A,G,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2362471,G,A,194,0.085,194,0.085,0,0,0,0,0,1,0,0,0,0,0.109
2L,2362480,C,T,2193,0.96,91,0.04,1,1,1,1,1,1,1,1,1,1,0.879
2L,2363150,G,C,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2366177,C,T,2119,0.928,165,0.072,1,1,1,1,1,1,1,1,1,1,0.763
2L,2366246,G,A,91,0.04,91,0.04,0,0,0,0,0,0,0,0.006,0.973,1,0.013
2L,2366253,T,A,91,0.04,91,0.04,0,0,0,0,0,0,0,0,1,1,0.013
2L,2366286,A,C,91,0.04,91,0.04,0,0,0,0,0,0,0,0,1,1,0.013
2L,2366310,G,A,194,0.085,194,0.085,0,0,0,0,0,1,0,0,0,0,0.107
2L,2366395,G,A,192,0.084,192,0.084,0,0,0,0,0,0.991,0,0,0,0,0.106
2L,2366481,A,G,130,0.057,130,0.057,0,0,0,0,0,1,0,0,0,0,0.016
2L,2366584,A,T,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2366774,T,A,109,0.048,109,0.048,0,0,0,0,0,0,0,0,0,0,0.163
2L,2366940,G,A,205,0.09,205,0.09,0,0,0,0,0,0.966,0,0,0,0,0.13
2L,2366951,A,C,108,0.047,108,0.047,0,0,0,0,0,0,0,0,0,0,0.161
2L,2368003,A,C,194,0.085,194,0.085,0,0,0,0,0,1,0,0,0,0,0.107
2L,2368079,A,G,2211,0.968,73,0.032,1,1,1,1,1,1,1,1,1,1,0.893
2L,2368145,T,C,110,0.048,110,0.048,0,0,0,0,0,0,0,0,0,0,0.164
2L,2368149,G,C,70,0.031,70,0.031,0,0,0,0,0,0,0,0,0,0,0.101
2L,2368229,G,T,854,0.374,854,0.374,1,0,0,0,0,0,0,0,0,0,0.087
2L,2368998,A,T,100,0.044,100,0.044,0,0,0,0,0,0,1,0,0,0,0.003
2L,2369004,C,A,74,0.032,74,0.032,0,0,0,0,0,0,0,0,0,0,0.11
2L,2369039,C,A,108,0.047,108,0.047,0,0,0,0,0,0,0,0,0,0,0.161
2L,2369050,G,C,855,0.374,855,0.374,1,0,0,0,0,0,0,0,0,0,0.088
2L,2369080,G,A,108,0.047,108,0.047,0,0,0,0,0,0,0,0,0,0,0.161
2L,2374622,T,G,108,0.047,108,0.047,0,0,0,0,0,0,0,0,0,0,0.161
2L,2374635,G,T,108,0.047,108,0.047,0,0,0,0,0,0,0,0,0,0,0.161
2L,2374654,T,G,382,0.167,382,0.167,0,1,0,0,0,0,1,1,0,0,0.121
2L,2374725,A,G,108,0.047,108,0.047,0,0,0,0,0,0,0,0,0,0,0.161
2L,2374735,T,A,108,0.047,108,0.047,0,0,0,0,0,0,0,0,0,0,0.161
2L,2374750,T,A,82,0.036,82,0.036,0,0,0,0,0,0,0,0,0,0,0.118
2L,2374751,A,T,82,0.036,82,0.036,0,0,0,0,0,0,0,0,0,0,0.118
2L,2374755,T,C,61,0.027,61,0.027,0,0,0,0,0,0,0,0,0,0,0.091
2L,2374773,C,T,108,0.047,108,0.047,0,0,0,0,0,0,0,0,0,0,0.161
2L,2374779,A,T,2193,0.96,91,0.04,0.999,1,1,1,1,1,1,1,1,1,0.875
2L,2374790,A,G,218,0.095,218,0.095,0,0,0,0,1,0,0,0,0,0,0.022
2L,2374798,A,G,921,0.403,921,0.403,0,1,1,1,1,0,1,1,1,1,0.355
2L,2374826,G,A,394,0.173,394,0.173,0,1,0,0,0,0,1,1,0,0,0.139
2L,2374869,T,C,97,0.042,97,0.042,0,0,0,0,0,0,0,0,0,0,0.139
2L,2374904,T,A,90,0.039,90,0.039,0,0,0,0,0,0,0,0,0,0,0.134
2L,2374917,T,A,2206,0.966,78,0.034,1,1,1,1,1,1,1,1,1,1,0.885
2L,2375026,A,C,87,0.038,87,0.038,0,0,0,0,0,0,0,0,0,0,0.125
2L,2375032,G,A,195,0.085,195,0.085,0,0,0,0,0,1,0,0,0,0,0.11
2L,2375098,C,A,2100,0.919,184,0.081,1,1,1,1,1,1,1,1,1,1,0.74
2L,2375312,G,T,196,0.086,196,0.086,0,0,0,0,0,1,0,0,0,0,0.107
2L,2375326,A,G,381,0.167,381,0.167,0,1,0,0,0,0,1,1,0,0,0.119
2L,2375534,T,G,1991,0.872,293,0.128,1,1,1,1,1,1,1,1,1,1,0.581
2L,2375571,C,T,1112,0.487,1112,0.487,0,1,1,1,1,1,1,1,1,1,0.457
2L,2375714,C,A,107,0.047,107,0.047,0,0,0,0,0,0,0,0,0,0,0.16
2L,2375761,T,C,108,0.047,108,0.047,0,0,0,0,0,0,0,0,0,0,0.161
2L,2375818,T,C,108,0.047,108,0.047,0,0,0,0,0,0,0,0,0,0,0.161
2L,2375891,A,T,109,0.048,109,0.048,0,0,0,0,0,0,0,0,0,0,0.161
2L,2375927,T,A,2221,0.972,63,0.028,1,1,1,1,1,1,1,1,1,1,0.909
2L,2375939,T,A,107,0.047,107,0.047,0,0,0,0,0,0,0,0,0,0,0.16
2L,2375956,A,G,108,0.047,108,0.047,0,0,0,0,0,0,0,0,0,0,0.161
2L,2375973,T,C,105,0.046,105,0.046,0,0,0,0,0,0,0,0,0,0,0.157
2L,2376095,C,G,132,0.058,132,0.058,0,0,0,0,0,0,0,0,1,1,0.072
2L,2376161,C,G,806,0.353,806,0.353,1,0,0,0,0,0,0,0,0,0,0.016
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2L,2440600,A,G,2001,0.876,283,0.124,0.997,1,1,1,1,1,1,1,1,1,0.596
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