##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##fileDate=20240124
##reference=reference.fa
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
##INFO=<ID=STRANDS,Number=.,Type=String,Description="Strand orientation of the adjacency in BEDPE format (DEL:+-, DUP:-+, INV:++/--)">
##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation">
##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
##INFO=<ID=CIPOS95,Number=2,Type=Integer,Description="Confidence interval (95%) around POS for imprecise variants">
##INFO=<ID=CIEND95,Number=2,Type=Integer,Description="Confidence interval (95%) around END for imprecise variants">
##INFO=<ID=MATEID,Number=.,Type=String,Description="ID of mate breakends">
##INFO=<ID=EVENT,Number=1,Type=String,Description="ID of event associated to breakend">
##INFO=<ID=SECONDARY,Number=0,Type=Flag,Description="Secondary breakend in a multi-line variants">
##INFO=<ID=SU,Number=.,Type=Integer,Description="Number of pieces of evidence supporting the variant across all samples">
##INFO=<ID=PE,Number=.,Type=Integer,Description="Number of paired-end reads supporting the variant across all samples">
##INFO=<ID=SR,Number=.,Type=Integer,Description="Number of split reads supporting the variant across all samples">
##INFO=<ID=BD,Number=.,Type=Integer,Description="Amount of BED evidence supporting the variant across all samples">
##INFO=<ID=EV,Number=.,Type=String,Description="Type of LUMPY evidence contributing to the variant call">
##INFO=<ID=PRPOS,Number=.,Type=String,Description="LUMPY probability curve of the POS breakend">
##INFO=<ID=PREND,Number=.,Type=String,Description="LUMPY probability curve of the END breakend">
##ALT=<ID=DEL,Description="Deletion">
##ALT=<ID=DUP,Description="Duplication">
##ALT=<ID=INV,Description="Inversion">
##ALT=<ID=DUP:TANDEM,Description="Tandem duplication">
##ALT=<ID=INS,Description="Insertion of novel sequence">
##ALT=<ID=CNV,Description="Copy number variable region">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=SU,Number=1,Type=Integer,Description="Number of pieces of evidence supporting the variant">
##FORMAT=<ID=PE,Number=1,Type=Integer,Description="Number of paired-end reads supporting the variant">
##FORMAT=<ID=SR,Number=1,Type=Integer,Description="Number of split reads supporting the variant">
##FORMAT=<ID=BD,Number=1,Type=Integer,Description="Amount of BED evidence supporting the variant">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype quality">
##FORMAT=<ID=SQ,Number=1,Type=Float,Description="Phred-scaled probability that this site is variant (non-reference in this sample">
##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood, log10-scaled likelihoods of the data given the called genotype for each possible genotype generated from the reference and alternate alleles given the sample ploidy">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read depth">
##FORMAT=<ID=RO,Number=1,Type=Integer,Description="Reference allele observation count, with partial observations recorded fractionally">
##FORMAT=<ID=AO,Number=A,Type=Integer,Description="Alternate allele observations, with partial observations recorded fractionally">
##FORMAT=<ID=QR,Number=1,Type=Integer,Description="Sum of quality of reference observations">
##FORMAT=<ID=QA,Number=A,Type=Integer,Description="Sum of quality of alternate observations">
##FORMAT=<ID=RS,Number=1,Type=Integer,Description="Reference allele split-read observation count, with partial observations recorded fractionally">
##FORMAT=<ID=AS,Number=A,Type=Integer,Description="Alternate allele split-read observation count, with partial observations recorded fractionally">
##FORMAT=<ID=ASC,Number=A,Type=Integer,Description="Alternate allele clipped-read observation count, with partial observations recorded fractionally">
##FORMAT=<ID=RP,Number=1,Type=Integer,Description="Reference allele paired-end observation count, with partial observations recorded fractionally">
##FORMAT=<ID=AP,Number=A,Type=Integer,Description="Alternate allele paired-end observation count, with partial observations recorded fractionally">
##FORMAT=<ID=AB,Number=A,Type=Float,Description="Allele balance, fraction of observations from alternate allele, QA/(QR+QA)">
##contig=<ID=chrI_sub,length=100000>
##smoove_version=0.2.8
##smoove_count_stats=RG1:0,638,0,598
##smoove_count_stats=RG2:0,466,0,448
##source=LUMPY
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##bcftools_viewVersion=1.17+htslib-1.17
##bcftools_viewCommand=view -O z -c 1 -o output-smoove.genotyped.vcf.gz; Date=Wed Jan 24 19:27:57 2024
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	RG1	RG2
chrI_sub	50007	1	N	<DUP>	103.66	.	SVTYPE=DUP;SVLEN=1148;END=51155;STRANDS=-+:5;IMPRECISE;CIPOS=0,22;CIEND=-30,331;CIPOS95=0,10;CIEND95=-10,82;SU=5;PE=5;SR=0;PRPOS=0.258039,0.191959,0.142119,0.105597,0.0777833,0.0578014,0.0427846,0.032024,0.023764,0.0176738,0.0130831,0.00982276,0.00731486,0.00542727,0.00399758,0.00297292,0.00221878,0.00165017,0.00122989,0.000915475,0.000674295,0.000501964,0.000370575;PREND=5.85377e-06,7.73803e-06,1.03845e-05,1.38061e-05,1.83274e-05,2.4271e-05,3.24374e-05,4.32758e-05,5.77075e-05,7.68205e-05,0.000102643,0.000137372,0.000184925,0.00024509,0.000329301,0.000440606,0.000583882,0.000773449,0.00103874,0.00137293,0.0018211,0.00244098,0.0032246,0.00433051,0.00577701,0.00771097,0.0100947,0.0134638,0.017428,0.023191,0.0297785,0.0287776,0.0271433,0.0260442,0.0251005,0.0239221,0.0226973,0.022123,0.0207745,0.0198427,0.0190339,0.0181385,0.0179065,0.0174155,0.0168898,0.0165094,0.0157197,0.015398,0.0149506,0.0147207,0.014548,0.0142966,0.0140289,0.0136684,0.0132831,0.013124,0.0126578,0.0124307,0.0121283,0.0114912,0.0113024,0.0110801,0.0107855,0.0107408,0.0105719,0.010252,0.0100385,0.00989579,0.00964551,0.00952156,0.00917511,0.00901622,0.0089231,0.00872881,0.00852142,0.00828831,0.00796058,0.00770706,0.00751548,0.00708522,0.00687959,0.00654007,0.0063474,0.00626172,0.00607514,0.00598551,0.00572162,0.00547532,0.00517031,0.00507122,0.00476895,0.00459012,0.00440836,0.00415379,0.00393712,0.00382996,0.00364121,0.00353575,0.00342231,0.00315652,0.00304452,0.00290783,0.00272193,0.00266152,0.00248906,0.00233477,0.00230558,0.00218745,0.00210921,0.00208486,0.00195023,0.00191344,0.00188952,0.00177463,0.00176537,0.00165498,0.00159982,0.00154295,0.00152936,0.00151581,0.00148667,0.00136872,0.00133499,0.00122388,0.00117244,0.00114374,0.00109766,0.00105654,0.00102599,0.000908013,0.00089917,0.000841279,0.000780186,0.000748484,0.000704024,0.000674257,0.000641784,0.000584102,0.000563501,0.000540792,0.000519593,0.000507932,0.000498128,0.000471617,0.000459362,0.000446368,0.000438032,0.000435269,0.000425232,0.000401305,0.00038503,0.000357298,0.000347914,0.000330873,0.000326613,0.000317727,0.00029779,0.000277006,0.000261571,0.000246701,0.00023847,0.000227691,0.000216491,0.000207228,0.000194862,0.000188863,0.000183536,0.000181414,0.000168119,0.000161592,0.000152474,0.000150676,0.00014958,0.000147849,0.00014255,0.000141498,0.000136699,0.000135359,0.000130407,0.000124551,0.000118969,0.000112593,0.000109014,0.000105885,0.000101976,0.000101471,9.81661e-05,9.4903e-05,9.33805e-05,8.92603e-05,8.5718e-05,8.43405e-05,8.43405e-05,7.83631e-05,7.77206e-05,7.24593e-05,7.20819e-05,6.92001e-05,6.88047e-05,6.45869e-05,5.93805e-05,5.39222e-05,5.04172e-05,4.97203e-05,4.78039e-05,4.40517e-05,4.07077e-05,3.76779e-05,3.26187e-05,3.09886e-05,2.94952e-05,2.81091e-05,2.67635e-05,2.55503e-05,2.44152e-05,2.44152e-05,2.31509e-05,2.20697e-05,2.16647e-05,1.9562e-05,1.89572e-05,1.73377e-05,1.68284e-05,1.56743e-05,1.54104e-05,1.44891e-05,1.44455e-05,1.24429e-05,1.21889e-05,1.15144e-05,1.1345e-05,1.06711e-05,1.05578e-05,1.04779e-05,9.85417e-06,8.85111e-06,7.89968e-06,7.4231e-06,6.88815e-06,6.86571e-06,6.76755e-06,6.74529e-06,6.38168e-06,5.57945e-06,5.28579e-06,4.95863e-06,4.82984e-06,4.81336e-06,4.77422e-06,4.66379e-06,4.59303e-06,4.28648e-06,4.25661e-06,4.19686e-06,3.40704e-06,3.37014e-06,2.74502e-06,2.73489e-06,2.53014e-06,2.51133e-06,2.27525e-06,2.24712e-06,1.83448e-06,1.65944e-06,1.65308e-06,1.37572e-06,1.25623e-06,1.13226e-06,1.1278e-06,1.11313e-06,9.94694e-07,8.85533e-07,7.94148e-07,7.25022e-07,6.40991e-07,6.40991e-07,5.66608e-07,5.66608e-07,5.04999e-07,4.97883e-07,4.858e-07,4.858e-07,4.3091e-07,4.10457e-07,4.04316e-07,3.96503e-07,3.90456e-07,3.41062e-07,3.34301e-07,2.87897e-07,2.86605e-07,2.78756e-07,2.71737e-07,2.66751e-07,2.5482e-07,2.2371e-07,2.19872e-07,2.12274e-07,2.12274e-07,2.11258e-07,2.08515e-07,2.07512e-07,2.03502e-07,2.025e-07,2.01497e-07,1.7167e-07,1.70816e-07,1.44698e-07,1.43971e-07,1.02317e-07,1.02317e-07,7.27124e-08,7.0605e-08,5.82493e-08,5.76361e-08,5.76361e-08,5.59409e-08,3.89337e-08,3.87244e-08,3.79226e-08,3.77165e-08,3.59485e-08,2.87588e-08,2.79782e-08,2.16365e-08,2.16365e-08,2.11459e-08,2.05441e-08,1.99506e-08,1.93652e-08,1.54922e-08,1.54032e-08,1.52251e-08,1.48557e-08,1.45936e-08,1.45062e-08,1.44188e-08,1.43314e-08,1.43314e-08,1.43314e-08,6.94477e-09,6.67767e-09,3.21146e-09,3.14592e-09,3.12614e-09,3.04164e-09,3.04164e-09,3.04164e-09,1.46002e-09,1.40973e-09,1.40046e-09,1.40046e-09,1.36027e-09,1.32049e-09,1.27247e-09,6.36233e-10,6.31905e-10,3.0946e-10,2.9998e-10,2.97867e-10,2.90602e-10,2.90602e-10;AC=4;AN=4	GT:GQ:SQ:GL:DP:RO:AO:QR:QA:RS:AS:ASC:RP:AP:AB	1/1:10:74.81:-9,-3,-2:7:1:5:1:5:0:0:0:1:5:0.83	1/1:2:28.84:-3,-1,-1:5:2:2:2:2:0:0:0:2:2:0.5