Supplementary Table 3. Population allele frequencies of all variant positions,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,, CHROM,POS,REF,ALT_1,ALT_2,ALT_3,ALT_AC_1,ALT_AC_2,ALT_AC_3,FILTER_PASS,AF_REF_GHcol,AF_ALT1_GHcol,AF_ALT2_GHcol,AF_ALT3_GHcol,AF_REF_GHgam,AF_ALT1_GHgam,AF_ALT2_GHgam,AF_ALT3_GHgam,AF_REF_BFgam,AF_ALT1_BFgam,AF_ALT2_BFgam,AF_ALT3_BFgam,AF_REF_BFcol,AF_ALT1_BFcol,AF_ALT2_BFcol,AF_ALT3_BFcol,AF_REF_UGgam,AF_ALT1_UGgam,AF_ALT2_UGgam,AF_ALT3_UGgam,AF_REF_GM,AF_ALT1_GM,AF_ALT2_GM,AF_ALT3_GM,AF_REF_GW,AF_ALT1_GW,AF_ALT2_GW,AF_ALT3_GW,AF_REF_KE,AF_ALT1_KE,AF_ALT2_KE,AF_ALT3_KE,AF_REF_CMgam,AF_ALT1_CMgam,AF_ALT2_CMgam,AF_ALT3_CMgam,AF_REF_FRgam,AF_ALT1_FRgam,AF_ALT2_FRgam,AF_ALT3_FRgam,AF_REF_GQgam,AF_ALT1_GQgam,AF_ALT2_GQgam,AF_ALT3_GQgam,AF_REF_AOcol,AF_ALT1_AOcol,AF_ALT2_AOcol,AF_ALT3_AOcol,AF_REF_GAgam,AF_ALT1_GAgam,AF_ALT2_GAgam,AF_ALT3_GAgam,AF_REF_GNgam,AF_ALT1_GNgam,AF_ALT2_GNgam,AF_ALT3_GNgam,AF_REF_GNcol,AF_ALT1_GNcol,AF_ALT2_GNcol,AF_ALT3_GNcol,AF_REF_CIcol,AF_ALT1_CIcol,AF_ALT2_CIcol,AF_ALT3_CIcol 2L,2348164,G,A,,,8,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.6665,0.3333,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348173,A,T,,,242,0,0,False,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0.1538,0.846,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0.0909,0.909,0,0 2L,2348189,T,C,,,124,0,0,False,0.3333,0.6665,0,0,0,1,0,0,0,1,0,0,0,1,0,0,1,0,0,0,0.5,0.5,0,0,0.952,0.0476,0,0,1,0,0,0,0.9414,0.05884,0,0,1,0,0,0,0,0,0,0,0.25,0.75,0,0,1,0,0,0,0,1,0,0,0,1,0,0,0.0714,0.9287,0,0 2L,2348199,T,A,,,3,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.5,0.5,0,0,0.978,0.02174,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348219,T,C,,,42,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.46,0.54,0,0,0.75,0.25,0,0,0.9136,0.0862,0,0,0.9165,0.0833,0,0,0.9463,0.05356,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348253,C,T,,,11,0,0,False,1,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0.9185,0.0814,0,0,0.857,0.1428,0,0,0.973,0.02702,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348258,G,C,,,6,0,0,False,1,0,0,0,0,0,0,0,0.976,0.0238,0,0,1,0,0,0,0.978,0.02174,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.976,0.0238,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348259,C,T,,,14,0,0,False,1,0,0,0,0,0,0,0,0.9536,0.0465,0,0,1,0,0,0,0.939,0.06122,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.9907,0.00917,0,0,1,0,0,0,1,0,0,0,0.976,0.0238,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348296,A,G,,,1246,0,0,False,0.04,0.96,0,0,0,1,0,0,0,1,0,0,0.03488,0.9653,0,0,0,1,0,0,0.125,0.875,0,0,0.11,0.89,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0.12036,0.8794,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0.05884,0.9414,0,0 2L,2348328,G,T,,,5,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,0.9546,0.04544,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348339,C,T,,,9,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.9263,0.0738,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348342,A,G,,,1,0,0,False,1,0,0,0,1,0,0,0,0.9937,0.00658,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348345,G,A,,,51,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.8706,0.1296,0,0,0.6885,0.3115,0,0,1,0,0,0,0.998,0.002008,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348348,A,G,,,1,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,0.9917,0.00848,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348355,C,G,,,1810,0,0,False,0.02856,0.971,0,0,0,1,0,0,0,1,0,0,0.041,0.959,0,0,0,1,0,0,0.0714,0.9287,0,0,0.1528,0.847,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0.1666,0.8335,0,0,0.1346,0.865,0,0 2L,2348368,C,T,,,19,0,0,False,1,0,0,0,1,0,0,0,0.994,0.00568,0,0,0.9844,0.01538,0,0,0.995,0.004856,0,0,1,0,0,0,0.974,0.02597,0,0,1,0,0,0,1,0,0,0,0.881,0.119,0,0,0.8887,0.1111,0,0,0.97,0.02985,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348371,C,A,,,3,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.9946,0.005596,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348405,A,T,,,12,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.978,0.02174,0,0,1,0,0,0,1,0,0,0,0.993,0.0068,0,0,0.896,0.1042,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.987,0.01316,0,0,1,0,0,0,1,0,0,0 2L,2348412,T,A,,,1,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.994,0.00568,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348421,C,T,,,86,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.7754,0.2245,0,0,0.636,0.3635,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348454,G,A,,,1,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.9946,0.005493,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348456,C,A,,,3,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.9946,0.005493,0,0,1,0,0,0,0.9985,0.001683,0,0,1,0,0,0,1,0,0,0,0.9937,0.00641,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348458,G,A,,,4,0,0,False,1,0,0,0,1,0,0,0,0.9946,0.005436,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.9946,0.005493,0,0,0.9897,0.010414,0,0,0.9985,0.001683,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348459,G,A,,,5,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.9985,0.001683,0,0,1,0,0,0,1,0,0,0,0.9873,0.01282,0,0,0.9927,0.007355,0,0,0.9873,0.0125,0,0,1,0,0,0,1,0,0,0 2L,2348465,C,T,,,104,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,0.993,0.006668,0,0,1,0,0,0,0.782,0.2178,0,0,0.5825,0.4175,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348484,C,T,,,2,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.9985,0.001683,0,0,1,0,0,0,0.9443,0.05554,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348492,G,T,,,2,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.9956,0.004463,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.9985,0.001683,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348597,A,C,,,9,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.9844,0.01538,0,0,0.9614,0.03845,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348600,G,A,,,9,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.9844,0.01538,0,0,0.9614,0.03845,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348601,T,A,C,,8,1,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.9844,0.01538,0,0,0.967,0.03296,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.993,0,0.007042,0 2L,2348602,T,C,,,9,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.9844,0.01538,0,0,0.9614,0.03845,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348607,A,T,,,8,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.9844,0.01538,0,0,0.967,0.03296,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348612,T,G,,,7,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.9844,0.01538,0,0,0.9727,0.02747,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348614,T,C,,,8,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.9844,0.01538,0,0,0.967,0.03296,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 2L,2348621,G,A,,,111,0,0,False,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,0.7383,0.2615,0,0,0.577,0.423,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0,1,0,0,0 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