Why REF = N?

[robertzeibich]

Do you know why for the REF N is displayed? Is there also a way to obtain the ALT sequence?

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT GALF003
chr1 789502 440 N 87.49 . SVTYPE=DUP;SVLEN=223225049;END=224014551;STRANDS=-+:9;IMPRECISE;CIPOS=-407,29;CIEND=-30,342;CIPOS95=-100,7;CIEND95=-9,72;SU=9;PE=9;SR=0;PRPOS=3.61176e-16,4.1447e-16,4.74956e-16,5.44
769e-16,6.24786e-16,7.14135e-16,8.18997e-16,9.37485e-16,1.07223e-15,1.23006e-15,1.40581e-15,1.60444e-15,1.83034e-15,2.0893e-15,2.38585e-15,2.73204e-15,3.11754e-15,3.55584e-15,4.07309e-15,4.66368e-15,5.30318e-15,6.04938e-15,6.89666e-15,7.
84477e-15,8.9712e-15,1.02639e-14,1.16718e-14,1.33188e-14,1.51842e-14,1.73273e-14,1.97681e-14,2.24816e-14,2.56338e-14,2.92283e-14,3.31236e-14,3.76362e-14,4.27849e-14,4.87925e-14,5.54265e-14,6.29927e-14,7.17939e-14,8.16114e-14,9.29521e-14,
1.05538e-13,1.19858e-13,1.3633e-13,1.54996e-13,1.7624e-13,2.00383e-13,2.27962e-13,2.58967e-13,2.94094e-13,3.34295e-13,3.79576e-13,4.30449e-13,4.88936e-13,5.54634e-13,6.28493e-13,7.12433e-13,8.06341e-13,9.14775e-13,1.03816e-12,1.17942e-12
,1.33588e-12,1.51284e-12,1.71588e-12,1.94014e-12,2.19536e-12,2.48849e-12,2.8176e-12,3.19156e-12,3.61295e-12,4.09749e-12,4.63506e-12,5.23569e-12,5.90984e-12,6.66949e-12,7.53358e-12,8.50361e-12,9.58996e-12,1.08349e-11,1.22514e-11,1.38513e-
11,1.56106e-11,1.75759e-11,1.98029e-11,2.23272e-11,2.51982e-11,2.84035e-11,3.20029e-11,3.6102e-11,4.07211e-11,4.57662e-11,5.16214e-11,5.8198e-11,6.55702e-11,7.38379e-11,8.30524e-11,9.35058e-11,1.05157e-10,1.18174e-10,1.32631e-10,1.49218e
-10,1.67506e-10,1.88088e-10,2.10759e-10,2.36248e-10,2.64904e-10,2.9696e-10,3.33462e-10,3.74279e-10,4.20026e-10,4.72008e-10,5.29035e-10,5.91764e-10,6.62178e-10,7.40784e-10,8.30626e-10,9.29138e-10,1.03966e-09,1.164e-09,1.30251e-09,1.45577e
-09,1.62608e-09,1.81718e-09,2.02931e-09,2.26863e-09,2.53223e-09,2.82628e-09,3.15087e-09,3.5125e-09,3.91974e-09,4.36553e-09,4.87152e-09,5.43103e-09,6.04468e-09,6.72957e-09,7.4896e-09,8.32004e-09,9.25559e-09,1.02913e-08,1.14478e-08,1.27413
e-08,1.41467e-08,1.57108e-08,1.74288e-08,1.93361e-08,2.14579e-08,2.37482e-08,2.63339e-08,2.91842e-08,3.23291e-08,3.58087e-08,3.96582e-08,4.39173e-08,4.86081e-08,5.38182e-08,5.94971e-08,6.57946e-08,7.26647e-08,8.0325e-08,8.87347e-08,9.795
97e-08,1.07967e-07,1.19279e-07,1.31607e-07,1.45188e-07,1.60131e-07,1.76448e-07,1.94381e-07,2.13763e-07,2.35198e-07,2.58562e-07,2.8413e-07,3.12611e-07,3.43549e-07,3.7768e-07,4.14696e-07,4.54849e-07,4.9918e-07,5.47651e-07,6.01038e-07,6.584
74e-07,7.21179e-07,7.89896e-07,8.65879e-07,9.48594e-07,1.03712e-06,1.13256e-06,1.23853e-06,1.35299e-06,1.47761e-06,1.61226e-06,1.75903e-06,1.91839e-06,2.09334e-06,2.28295e-06,2.48822e-06,2.71128e-06,2.95126e-06,3.20845e-06,3.48639e-06,3.
7888e-06,4.1147e-06,4.47091e-06,4.85626e-06,5.2748e-06,5.72447e-06,6.21155e-06,6.73021e-06,7.29079e-06,7.89311e-06,8.54353e-06,9.24185e-06,9.9887e-06,1.07971e-05,1.1675e-05,1.26072e-05,1.36167e-05,1.46903e-05,1.58406e-05,1.70856e-05,1.83
927e-05,1.98104e-05,2.131e-05,2.29243e-05,2.4674e-05,2.65282e-05,2.84976e-05,3.06317e-05,3.28748e-05,3.52793e-05,3.78224e-05,4.05117e-05,4.33912e-05,4.64374e-05,4.9707e-05,5.31926e-05,5.69078e-05,6.08353e-05,6.49653e-05,6.93284e-05,7.401
19e-05,7.89789e-05,8.42232e-05,8.97375e-05,9.55925e-05,0.000101789,0.000108471,0.00011543,0.000122766,0.000130536,0.000138579,0.000147094,0.000156098,0.000165527,0.000175615,0.000186187,0.000197188,0.000208763,0.000221019,0.000233878,0.0
00247356,0.000261312,0.000276207,0.000291507,0.000307761,0.000324712,0.000342364,0.00036121,0.000380501,0.000400555,0.000421519,0.000443804,0.000466721,0.00049053,0.000515402,0.00054154,0.000569068,0.00059741,0.000626901,0.000657476,0.00
0689234,0.000722091,0.000756564,0.000792274,0.000829153,0.000867633,0.000907816,0.000949561,0.000992297,0.00103698,0.00108272,0.00113011,0.00117965,0.0012298,0.00128233,0.00133644,0.00139219,0.00144985,0.00150914,0.00157076,0.0016341,0.0
0169893,0.00176572,0.00183505,0.00190604,0.00197849,0.00205368,0.00213198,0.00221258,0.00229426,0.00237776,0.00246492,0.00255305,0.0026435,0.00273666,0.00283237,0.00292979,0.00303047,0.00313313,0.00323913,0.00334737,0.00345735,0.00356825
,0.00368173,0.00379801,0.00391568,0.00403717,0.00416067,0.00428632,0.00441581,0.00454542,0.00467785,0.00481304,0.00495118,0.00509041,0.00523101,0.00537412,0.00551889,0.00566833,0.0058193,0.00597374,0.00612914,0.00628634,0.00644548,0.0066
0766,0.00677086,0.00693499,0.00710248,0.00727294,0.00744573,0.00761905,0.00779529,0.00797086,0.00814758,0.00832652,0.00850617,0.00868607,0.00886919,0.00905285,0.00923939,0.00942782,0.00961457,0.00980094,0.00998996,0.0101773,0.0103638,0.0
105532,0.010742,0.0109339,0.0111259,0.0113175,0.0115107,0.011704,0.0118972,0.0120908,0.012281,0.0124716,0.0126608,0.0128505,0.0130428,0.0132351,0.0134266,0.0136173,0.0138048,0.0139936,0.0141807,0.0143651,0.0145482,0.0147292,0.0149081,0.0
150864,0.0152648,0.0154444,0.0156191,0.0157927,0.0159669,0.0161369,0.0163032,0.0164712,0.0166379,0.0168019,0.0169616,0.0171198,0.0172794,0.017435,0.0175878,0.0130494,0.00968088,0.00717864,0.00532287,0.00394662,0.00292602,0.00216877,0.001
60704,0.00119074,0.000882033,0.000653317,0.000483776,0.000263488,0.000143486,7.81259e-05,4.253e-05,2.31517e-05,1.26021e-05,6.85862e-06,3.73198e-06,1.49351e-06,5.97619e-07,2.39116e-07,9.56484e-08,3.82587e-08,1.53021e-08,6.11971e-09,2.4471
1e-09,9.78429e-10;PREND=5.36587e-06,7.16389e-06,9.56719e-06,1.27735e-05,1.70482e-05,2.27495e-05,3.03568e-05,4.05006e-05,5.40226e-05,7.20381e-05,9.60398e-05,0.000127996,0.000170534,0.00022709,0.000302425,0.000402782,0.000536295,0.00071409
2,0.000950311,0.00126395,0.00168103,0.00223589,0.0029718,0.00394893,0.00524633,0.00697082,0.00925984,0.0122998,0.0163354,0.0216814,0.0287724,0.0280738,0.0273884,0.0267124,0.0260538,0.0254035,0.0247661,0.0241375,0.023506,0.0228962,0.02228
63,0.0216852,0.0211025,0.0205224,0.0199607,0.0193993,0.0188583,0.0183219,0.0178008,0.0172918,0.0167917,0.016295,0.0158082,0.0153288,0.0148614,0.0144068,0.0139595,0.0135223,0.0130952,0.0126749,0.0122662,0.0118745,0.0114884,0.0111055,0.010
7322,0.0103688,0.0100186,0.00967532,0.00933965,0.00901685,0.00870031,0.00839453,0.00808941,0.00779345,0.00750763,0.00722911,0.00695828,0.00669712,0.00644401,0.00619804,0.00596105,0.00572738,0.00550191,0.00528584,0.00507362,0.00486757,0.0
0466619,0.00447514,0.00429028,0.00411176,0.00394034,0.00377302,0.00361025,0.00345255,0.00330167,0.00315745,0.00301719,0.0028836,0.00275518,0.00263005,0.00251024,0.00239538,0.00228382,0.00217625,0.00207349,0.00197451,0.00187968,0.00178902
,0.00170363,0.0016208,0.00154157,0.00146569,0.00139248,0.00132268,0.00125586,0.00119099,0.00112929,0.00107041,0.0010145,0.000961953,0.00091078,0.00086238,0.000816503,0.000772849,0.000730519,0.000690024,0.000651269,0.000614694,0.000580047
,0.00054759,0.000516865,0.000488057,0.000460495,0.000433758,0.000408518,0.000384555,0.000361563,0.00033981,0.000319494,0.000300212,0.000282052,0.00026502,0.000249008,0.000233739,0.000219376,0.000205801,0.000192805,0.000180559,0.000168989
,0.000158252,0.000148098,0.000138509,0.000129569,0.000121205,0.000113309,0.000105894,9.88867e-05,9.23368e-05,8.61122e-05,8.03595e-05,7.48394e-05,6.96976e-05,6.49231e-05,6.04876e-05,5.63523e-05,5.23928e-05,4.87459e-05,4.53227e-05,4.20825e
-05,3.90993e-05,3.62931e-05,3.36723e-05,3.12406e-05,2.89835e-05,2.68425e-05,2.48946e-05,2.30242e-05,2.13049e-05,1.97283e-05,1.82477e-05,1.68647e-05,1.55782e-05,1.4383e-05,1.32867e-05,1.22801e-05,1.13333e-05,1.04685e-05,9.65008e-06,8.9038
2e-06,8.19636e-06,7.53966e-06,6.94665e-06,6.3897e-06,5.8837e-06,5.41065e-06,4.9758e-06,4.5755e-06,4.20499e-06,3.86016e-06,3.53972e-06,3.24836e-06,2.9813e-06,2.73458e-06,2.50892e-06,2.30096e-06,2.10778e-06,1.93024e-06,1.76705e-06,1.61557e
-06,1.47617e-06,1.3493e-06,1.23175e-06,1.12545e-06,1.02652e-06,9.37995e-07,8.56817e-07,7.8232e-07,7.13498e-07,6.50859e-07,5.92359e-07,5.39216e-07,4.90548e-07,4.46371e-07,4.05935e-07,3.69546e-07,3.36242e-07,3.05832e-07,2.78107e-07,2.52464
e-07,2.2938e-07,2.0803e-07,1.88952e-07,1.71149e-07,1.55276e-07,1.40687e-07,1.27456e-07,1.15693e-07,1.04851e-07,9.48102e-08,8.57512e-08,7.74587e-08,7.00348e-08,6.31858e-08,5.71125e-08,5.16287e-08,4.66095e-08,4.20858e-08,3.80766e-08,3.4393
1e-08,3.1019e-08,2.80018e-08,2.52491e-08,2.27594e-08,2.05057e-08,1.84337e-08,1.65903e-08,1.49392e-08,1.34583e-08,1.21413e-08,1.09349e-08,9.84008e-09,8.83815e-09,7.93515e-09,7.13822e-09,6.40898e-09,5.76769e-09,5.18088e-09,4.65729e-09,4.18
502e-09,3.74832e-09,3.36255e-09,3.00933e-09,2.69453e-09,2.41625e-09,2.16576e-09,1.93976e-09,1.73603e-09,1.55305e-09,1.39006e-09,1.24587e-09,1.11254e-09,9.95514e-10,8.89999e-10,7.93964e-10,7.08922e-10,6.33194e-10,5.65692e-10,5.04947e-10,4
.49874e-10,4.01197e-10,3.57682e-10,3.1938e-10,2.85048e-10,2.54196e-10,2.26946e-10,2.02038e-10,1.79384e-10,1.59841e-10,1.42608e-10,1.26802e-10,1.12775e-10,1.00272e-10,8.92358e-11,7.93657e-11,7.04809e-11,6.27029e-11,5.56967e-11,4.93595e-11
,4.39144e-11,3.90816e-11,3.48062e-11,3.0878e-11,2.7369e-11,2.43019e-11,2.14653e-11,1.90549e-11,1.69098e-11,1.49124e-11,1.32037e-11,1.1713e-11,1.03702e-11,9.1627e-12,8.09731e-12,7.137e-12,6.31599e-12,5.58015e-12,4.91209e-12,4.33341e-12,3.
81779e-12,3.36531e-12,2.96827e-12,2.62004e-12,2.30837e-12,2.02598e-12,1.78541e-12,1.57553e-12,1.39274e-12,1.22958e-12,1.08252e-12,9.54385e-13,8.37725e-13,7.35656e-13,6.46523e-13,5.68482e-13,4.98281e-13,4.38134e-13,3.84385e-13,3.35822e-13
,2.93054e-13,2.57514e-13,2.25816e-13,1.97535e-13,1.72186e-13,1.51964e-13,1.33552e-13,1.16865e-13,1.02073e-13,8.85409e-14,7.71834e-14,6.73974e-14,5.86775e-14,5.12343e-14,4.46918e-14,3.90221e-14,3.40168e-14,2.95843e-14,2.57152e-14,2.22386e
-14,1.94111e-14,1.68357e-14,1.47332e-14,1.28086e-14,1.11338e-14;AC=1;AN=2 GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB 0/1:6:87.49:-9,-1,-1:43:33:9:33:9:0:0:0:33:9:0.21

[pingxinxing]

Has this problem been solved? Whether my file is merged or VCF file after genotyping with --genotype, the column of REF is "N".