Testdata for IntervalStratification
This commit is contained in:
Mark DePristo
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dc4932f93d
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714cac21c9
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20 315000 315100 # should overlap 2 in withSymbolic.vcf at 315006 and 315072
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20 316955 316959 # should overlap only deletion variant at 316952
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20 317900 400000 # should overlap only the symbolic variant at 317173
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##fileformat=VCFv4.1
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##INFO=<ID=LCSNP,Number=0,Type=Flag,Description="Genotype likelihood in Low coverage VCF in data integration">
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##INFO=<ID=EXSNP,Number=0,Type=Flag,Description="Genotype likelihood in Exome VCF in data integration">
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##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Genotype likelihood in INDEL VCF in data integration">
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##INFO=<ID=SV,Number=0,Type=Flag,Description="Genotype likelihood in SV VCF in data integration">
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##INFO=<ID=BAVGPOST,Number=1,Type=Float,Description="Average posterior probability from beagle">
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##INFO=<ID=BRSQ,Number=1,Type=Float,Description="Genotype imputation quality estimate from beagle">
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##INFO=<ID=LDAF,Number=1,Type=Float,Description="MLE Allele Frequency Accounting for LD">
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##INFO=<ID=AVGPOST,Number=1,Type=Float,Description="Average posterior probability from MaCH/Thunder">
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##INFO=<ID=RSQ,Number=1,Type=Float,Description="Genotype imputation quality from MaCH/Thunder">
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##INFO=<ID=ERATE,Number=1,Type=Float,Description="Per-marker Mutation rate from MaCH/Thunder">
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##INFO=<ID=THETA,Number=1,Type=Float,Description="Per-marker Transition rate from MaCH/Thunder">
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##INFO=<ID=CIEND,Number=2,Type=Integer,Description="Confidence interval around END for imprecise variants">
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##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="Confidence interval around POS for imprecise variants">
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##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the variant described in this record">
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##INFO=<ID=HOMLEN,Number=.,Type=Integer,Description="Length of base pair identical micro-homology at event breakpoints">
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##INFO=<ID=HOMSEQ,Number=.,Type=String,Description="Sequence of base pair identical micro-homology at event breakpoints">
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##INFO=<ID=SOURCE,Number=.,Type=String,Description="Source of deletion call">
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##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Difference in length between REF and ALT alleles">
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##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
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##INFO=<ID=AC,Number=.,Type=Integer,Description="Alternate Allele Count">
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##INFO=<ID=AN,Number=1,Type=Integer,Description="Total Allele Count">
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##ALT=<ID=DEL,Description="Deletion">
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##FORMAT=<ID=DS,Number=1,Type=Float,Description="Genotype dosage from MaCH/Thunder">
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##FORMAT=<ID=GL,Number=.,Type=Float,Description="Genotype Likelihoods">
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##FORMAT=<ID=BD,Number=1,Type=Float,Description="Genotype dosage from beagle">
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#CHROM POS ID REF ALT QUAL FILTER INFO
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20 315006 . A G 100 PASS LCSNP;EXSNP;BAVGPOST=0.998;BRSQ=0.721;LDAF=0.0025;AVGPOST=0.9978;RSQ=0.6449;ERATE=0.0008;THETA=0.0006;AC=4;AN=2184
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20 315072 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.996;LDAF=0.0057;AVGPOST=0.9996;RSQ=0.9743;ERATE=0.0003;THETA=0.0016;AC=12;AN=2184
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20 315162 . T G 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.950;LDAF=0.0005;AVGPOST=0.9998;RSQ=0.8078;ERATE=0.0003;THETA=0.0004;AC=1;AN=2184
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20 315168 rs71327439 G GA 7142 PASS INDEL;BAVGPOST=0.999;BRSQ=0.990;LDAF=0.0575;AVGPOST=0.9985;RSQ=0.9891;ERATE=0.0003;THETA=0.0004;AC=125;AN=2184
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20 315201 . A G 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.965;LDAF=0.0005;AVGPOST=0.9999;RSQ=0.8599;ERATE=0.0003;THETA=0.0008;AC=1;AN=2184
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20 315214 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.974;LDAF=0.0009;AVGPOST=0.9990;RSQ=0.5860;ERATE=0.0003;THETA=0.0005;AC=1;AN=2184
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20 315270 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.999;LDAF=0.0557;AVGPOST=0.9992;RSQ=0.9950;ERATE=0.0003;THETA=0.0004;AC=121;AN=2184
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20 315279 . A G 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.991;LDAF=0.0572;AVGPOST=0.9990;RSQ=0.9926;ERATE=0.0003;THETA=0.0013;AC=125;AN=2184
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20 315320 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.995;LDAF=0.0028;AVGPOST=0.9998;RSQ=0.9594;ERATE=0.0005;THETA=0.0003;AC=6;AN=2184
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20 315322 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.814;LDAF=0.0007;AVGPOST=0.9994;RSQ=0.6510;ERATE=0.0003;THETA=0.0004;AC=1;AN=2184
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20 315431 . A T 100 PASS LCSNP;EXSNP;BAVGPOST=0.987;BRSQ=0.864;LDAF=0.0431;AVGPOST=0.9873;RSQ=0.8675;ERATE=0.0006;THETA=0.0010;AC=86;AN=2184
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20 315481 . T A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.998;LDAF=0.0619;AVGPOST=0.9993;RSQ=0.9948;ERATE=0.0003;THETA=0.0007;AC=135;AN=2184
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20 315490 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.984;LDAF=0.0138;AVGPOST=0.9971;RSQ=0.9260;ERATE=0.0003;THETA=0.0046;AC=31;AN=2184
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20 315523 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.822;LDAF=0.0015;AVGPOST=0.9988;RSQ=0.6777;ERATE=0.0005;THETA=0.0003;AC=2;AN=2184
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20 315547 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.893;LDAF=0.0026;AVGPOST=0.9995;RSQ=0.9024;ERATE=0.0003;THETA=0.0004;AC=5;AN=2184
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20 315549 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.888;LDAF=0.0029;AVGPOST=0.9988;RSQ=0.8565;ERATE=0.0003;THETA=0.0013;AC=5;AN=2184
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20 315551 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.829;LDAF=0.0008;AVGPOST=0.9992;RSQ=0.5723;ERATE=0.0003;THETA=0.0012;AC=1;AN=2184
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20 315704 . G C 100 PASS LCSNP;EXSNP;BAVGPOST=0.998;BRSQ=0.945;LDAF=0.0184;AVGPOST=0.9978;RSQ=0.9523;ERATE=0.0003;THETA=0.0017;AC=40;AN=2184
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20 315798 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.773;LDAF=0.0012;AVGPOST=0.9985;RSQ=0.4929;ERATE=0.0003;THETA=0.0005;AC=1;AN=2184
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20 315842 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.979;LDAF=0.0110;AVGPOST=0.9991;RSQ=0.9673;ERATE=0.0003;THETA=0.0005;AC=23;AN=2184
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20 315876 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.926;LDAF=0.0018;AVGPOST=0.9988;RSQ=0.7731;ERATE=0.0003;THETA=0.0007;AC=3;AN=2184
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20 316028 . G C 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.999;LDAF=0.0714;AVGPOST=0.9997;RSQ=0.9982;ERATE=0.0003;THETA=0.0003;AC=156;AN=2184
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20 316055 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.997;LDAF=0.1006;AVGPOST=0.9993;RSQ=0.9969;ERATE=0.0003;THETA=0.0007;AC=220;AN=2184
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20 316137 . G C 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.976;LDAF=0.0037;AVGPOST=0.9982;RSQ=0.7861;ERATE=0.0004;THETA=0.0009;AC=6;AN=2184
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20 316142 . C A 100 PASS LCSNP;EXSNP;BAVGPOST=0.998;BRSQ=0.793;LDAF=0.0033;AVGPOST=0.9980;RSQ=0.7527;ERATE=0.0003;THETA=0.0003;AC=6;AN=2184
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20 316143 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.839;LDAF=0.0034;AVGPOST=0.9984;RSQ=0.8054;ERATE=0.0003;THETA=0.0003;AC=6;AN=2184
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20 316211 . C G 100 PASS LCSNP;EXSNP;BAVGPOST=0.997;BRSQ=0.976;LDAF=0.0565;AVGPOST=0.9983;RSQ=0.9872;ERATE=0.0003;THETA=0.0010;AC=124;AN=2184
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20 316285 . A AT 5514 PASS INDEL;BAVGPOST=0.999;BRSQ=0.993;LDAF=0.0552;AVGPOST=0.9978;RSQ=0.9829;ERATE=0.0004;THETA=0.0005;AC=119;AN=2184
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20 316295 . A G 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.808;LDAF=0.0021;AVGPOST=0.9980;RSQ=0.6390;ERATE=0.0003;THETA=0.0008;AC=4;AN=2184
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20 316481 . G T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=1.000;LDAF=0.0499;AVGPOST=0.9997;RSQ=0.9970;ERATE=0.0003;THETA=0.0007;AC=109;AN=2184
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20 316488 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.897;LDAF=0.0011;AVGPOST=0.9997;RSQ=0.8509;ERATE=0.0003;THETA=0.0006;AC=2;AN=2184
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20 316553 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.945;LDAF=0.0007;AVGPOST=0.9996;RSQ=0.7074;ERATE=0.0003;THETA=0.0004;AC=1;AN=2184
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20 316659 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.998;LDAF=0.0497;AVGPOST=0.9995;RSQ=0.9960;ERATE=0.0003;THETA=0.0007;AC=109;AN=2184
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20 316691 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.985;LDAF=0.0058;AVGPOST=0.9989;RSQ=0.9301;ERATE=0.0003;THETA=0.0003;AC=13;AN=2184
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20 316700 . A G 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.737;LDAF=0.0030;AVGPOST=0.9971;RSQ=0.5700;ERATE=0.0009;THETA=0.0016;AC=4;AN=2184
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20 316725 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.853;LDAF=0.0011;AVGPOST=0.9995;RSQ=0.7944;ERATE=0.0003;THETA=0.0004;AC=2;AN=2184
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20 316770 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.966;LDAF=0.0017;AVGPOST=0.9991;RSQ=0.7543;ERATE=0.0005;THETA=0.0005;AC=3;AN=2184
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20 316813 . GTTC G 1701 PASS INDEL;BAVGPOST=0.995;BRSQ=0.850;LDAF=0.0156;AVGPOST=0.9987;RSQ=0.9611;ERATE=0.0003;THETA=0.0006;AC=34;AN=2184
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20 316824 rs11472305 T TTTC 5129 PASS INDEL;BAVGPOST=0.979;BRSQ=0.863;LDAF=0.0697;AVGPOST=0.9782;RSQ=0.8837;ERATE=0.0016;THETA=0.0006;AC=153;AN=2184
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20 316839 . CT C 1122 PASS INDEL;BAVGPOST=0.980;BRSQ=0.804;LDAF=0.0505;AVGPOST=0.9743;RSQ=0.8100;ERATE=0.0040;THETA=0.0009;AC=104;AN=2184
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20 316841 . TTC T 1096 PASS INDEL;BAVGPOST=0.981;BRSQ=0.824;LDAF=0.0491;AVGPOST=0.9783;RSQ=0.8367;ERATE=0.0029;THETA=0.0005;AC=105;AN=2184
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20 316842 . TCC T 110 PASS INDEL;BAVGPOST=0.983;BRSQ=0.592;LDAF=0.0203;AVGPOST=0.9772;RSQ=0.5576;ERATE=0.0022;THETA=0.0005;AC=30;AN=2184
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20 316845 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.645;LDAF=0.0015;AVGPOST=0.9989;RSQ=0.6666;ERATE=0.0003;THETA=0.0010;AC=2;AN=2184
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20 316853 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=0.990;BRSQ=0.922;LDAF=0.0688;AVGPOST=0.9742;RSQ=0.8456;ERATE=0.0049;THETA=0.0006;AC=133;AN=2184
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20 316882 rs11479165 CT C 145 PASS INDEL;BAVGPOST=0.991;BRSQ=0.484;LDAF=0.0074;AVGPOST=0.9920;RSQ=0.5655;ERATE=0.0005;THETA=0.0014;AC=9;AN=2184
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20 316889 . T TTC 108 PASS INDEL;BAVGPOST=0.978;BRSQ=0.235;LDAF=0.0521;AVGPOST=0.9304;RSQ=0.4479;ERATE=0.0035;THETA=0.0016;AC=63;AN=2184
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20 316901 . T TTC 272 PASS INDEL;BAVGPOST=0.979;BRSQ=0.510;LDAF=0.0363;AVGPOST=0.9527;RSQ=0.4348;ERATE=0.0071;THETA=0.0003;AC=34;AN=2184
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20 316917 . CT C 67 PASS INDEL;BAVGPOST=0.983;BRSQ=0.483;LDAF=0.0265;AVGPOST=0.9828;RSQ=0.7509;ERATE=0.0006;THETA=0.0011;AC=51;AN=2184
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20 316918 rs112071142 TTTC T 3049 PASS INDEL;BAVGPOST=0.980;BRSQ=0.801;LDAF=0.0588;AVGPOST=0.9761;RSQ=0.8444;ERATE=0.0026;THETA=0.0005;AC=120;AN=2184
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20 316924 . CT C 8 PASS INDEL;BAVGPOST=0.999;BRSQ=0.581;LDAF=0.0053;AVGPOST=0.9932;RSQ=0.5513;ERATE=0.0004;THETA=0.0011;AC=6;AN=2184
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20 316936 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=0.994;BRSQ=0.651;LDAF=0.0098;AVGPOST=0.9884;RSQ=0.5505;ERATE=0.0018;THETA=0.0005;AC=13;AN=2184
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20 316939 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=0.997;BRSQ=0.720;LDAF=0.0071;AVGPOST=0.9899;RSQ=0.4845;ERATE=0.0010;THETA=0.0033;AC=8;AN=2184
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20 316952 . CTCTTCCTCTTCT C 15835 PASS INDEL;BAVGPOST=0.891;BRSQ=0.667;LDAF=0.1650;AVGPOST=0.9042;RSQ=0.7274;ERATE=0.0037;THETA=0.0008;AC=294;AN=2184
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20 317003 . TCC T 333 PASS INDEL;BAVGPOST=0.890;BRSQ=0.114;LDAF=0.3450;AVGPOST=0.5526;RSQ=0.1674;ERATE=0.0300;THETA=0.0011;AC=350;AN=2184
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20 317022 rs111424933 TTTC T 4776 PASS INDEL;BAVGPOST=0.982;BRSQ=0.865;LDAF=0.0561;AVGPOST=0.9837;RSQ=0.8889;ERATE=0.0017;THETA=0.0004;AC=110;AN=2184
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20 317057 . C A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.775;LDAF=0.0014;AVGPOST=0.9985;RSQ=0.6049;ERATE=0.0003;THETA=0.0002;AC=3;AN=2184
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20 317135 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=0.995;BRSQ=0.992;LDAF=0.0489;AVGPOST=0.9964;RSQ=0.9749;ERATE=0.0004;THETA=0.0025;AC=106;AN=2184
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20 317173 MERGED_DEL_2_99440 A <DEL> . . SV;BAVGPOST=0.998;BRSQ=0.577;LDAF=0.0018;AVGPOST=0.9990;RSQ=0.7465;ERATE=0.0003;THETA=0.0007;CIEND=-61,92;CIPOS=-84,73;END=319201;SOURCE=BreakDancer_317182_319211,GenomeStrip_317164_319190;SVTYPE=DEL;AC=2;AN=2184
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20 317174 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=0.995;BRSQ=0.991;LDAF=0.0502;AVGPOST=0.9962;RSQ=0.9727;ERATE=0.0005;THETA=0.0007;AC=107;AN=2184
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20 317266 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.999;LDAF=0.1748;AVGPOST=0.9988;RSQ=0.9973;ERATE=0.0003;THETA=0.0005;AC=383;AN=2184
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20 317448 . A G 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.999;LDAF=0.0068;AVGPOST=0.9988;RSQ=0.9405;ERATE=0.0003;THETA=0.0002;AC=16;AN=2184
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20 317491 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=0.999;BRSQ=0.991;LDAF=0.0609;AVGPOST=0.9993;RSQ=0.9939;ERATE=0.0003;THETA=0.0004;AC=133;AN=2184
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20 317546 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.837;LDAF=0.0007;AVGPOST=0.9994;RSQ=0.6154;ERATE=0.0003;THETA=0.0012;AC=1;AN=2184
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20 317578 . C T 100 PASS LCSNP;EXSNP;BAVGPOST=0.996;BRSQ=0.882;LDAF=0.0180;AVGPOST=0.9981;RSQ=0.9606;ERATE=0.0003;THETA=0.0004;AC=40;AN=2184
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20 317658 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=1.000;LDAF=0.0609;AVGPOST=0.9998;RSQ=0.9980;ERATE=0.0003;THETA=0.0005;AC=133;AN=2184
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20 317676 . T C 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=1.000;LDAF=0.0608;AVGPOST=0.9999;RSQ=0.9992;ERATE=0.0003;THETA=0.0004;AC=133;AN=2184
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20 317710 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.952;LDAF=0.0014;AVGPOST=0.9997;RSQ=0.8880;ERATE=0.0004;THETA=0.0008;AC=3;AN=2184
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20 317824 . G A 100 PASS LCSNP;EXSNP;BAVGPOST=1.000;BRSQ=0.999;LDAF=0.0555;AVGPOST=0.9993;RSQ=0.9947;ERATE=0.0003;THETA=0.0009;AC=121;AN=2184
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