PrecisionFDA
Truth Challenge
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Explore HG002 comparison results
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| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
28301-28350 / 86044 show all | |||||||||||||||
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.8091 | 97.7471 | 99.8946 | 29.7927 | 1909 | 44 | 1895 | 2 | 2 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.1786 | 98.9124 | 99.4462 | 49.9692 | 1637 | 18 | 1616 | 9 | 2 | 22.2222 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | HG002complexvar | hetalt | 89.8660 | 82.0896 | 99.2701 | 60.2899 | 275 | 60 | 272 | 2 | 2 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 70.9091 | 60.0000 | 86.6667 | 81.7073 | 15 | 10 | 13 | 2 | 2 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 91.4566 | 84.8624 | 99.1620 | 69.5837 | 370 | 66 | 355 | 3 | 2 | 66.6667 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 86.4541 | 77.3273 | 98.0237 | 68.7461 | 515 | 151 | 496 | 10 | 2 | 20.0000 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 75.2215 | 62.0370 | 95.5224 | 69.6833 | 67 | 41 | 64 | 3 | 2 | 66.6667 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 86.7676 | 77.5281 | 98.5075 | 65.9033 | 138 | 40 | 132 | 2 | 2 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 81.6591 | 71.1864 | 95.7447 | 71.8563 | 42 | 17 | 45 | 2 | 2 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 86.4541 | 77.3273 | 98.0237 | 68.7461 | 515 | 151 | 496 | 10 | 2 | 20.0000 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 91.3706 | 85.7143 | 97.8261 | 63.1016 | 144 | 24 | 135 | 3 | 2 | 66.6667 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.4816 | 99.3427 | 99.6209 | 60.8825 | 1058 | 7 | 1051 | 4 | 2 | 50.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 95.7517 | 94.7955 | 96.7273 | 71.9674 | 255 | 14 | 266 | 9 | 2 | 22.2222 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 98.1641 | 97.2350 | 99.1111 | 53.7037 | 211 | 6 | 223 | 2 | 2 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | map_l100_m2_e0 | * | 98.0425 | 97.0760 | 99.0284 | 79.6316 | 1328 | 40 | 1325 | 13 | 2 | 15.3846 | |
| ltrigg-rtg2 | INDEL | I1_5 | map_l100_m2_e1 | * | 98.0445 | 97.1326 | 98.9736 | 79.7926 | 1355 | 40 | 1350 | 14 | 2 | 14.2857 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.5345 | 91.9028 | 97.3214 | 70.5650 | 227 | 20 | 218 | 6 | 2 | 33.3333 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 96.3154 | 93.3884 | 99.4318 | 53.2537 | 339 | 24 | 350 | 2 | 2 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.1262 | 97.3404 | 98.9247 | 60.0858 | 183 | 5 | 184 | 2 | 2 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.6185 | 96.2845 | 98.9899 | 65.5452 | 907 | 35 | 882 | 9 | 2 | 22.2222 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.6797 | 98.6928 | 98.6667 | 68.1529 | 151 | 2 | 148 | 2 | 2 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 97.3899 | 96.1290 | 98.6842 | 79.5699 | 149 | 6 | 150 | 2 | 2 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I6_15 | map_siren | * | 96.2876 | 93.7705 | 98.9437 | 78.2708 | 286 | 19 | 281 | 3 | 2 | 66.6667 | |
| ltrigg-rtg2 | INDEL | I6_15 | map_siren | homalt | 97.1812 | 96.6667 | 97.7011 | 75.2841 | 87 | 3 | 85 | 2 | 2 | 100.0000 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 94.1176 | 100.0000 | 88.8889 | 88.7500 | 15 | 0 | 16 | 2 | 2 | 100.0000 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.0901 | 99.5957 | 98.5896 | 55.8133 | 6159 | 25 | 6291 | 90 | 2 | 2.2222 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.6723 | 99.5675 | 97.7930 | 57.7847 | 3914 | 17 | 3988 | 90 | 2 | 2.2222 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 94.1176 | 100.0000 | 88.8889 | 88.7500 | 15 | 0 | 16 | 2 | 2 | 100.0000 | |
| ltrigg-rtg2 | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 84.0961 | 80.3922 | 88.1579 | 92.2449 | 82 | 20 | 67 | 9 | 2 | 22.2222 | |
| ltrigg-rtg2 | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.6003 | 99.6750 | 99.5257 | 31.5929 | 4601 | 15 | 4616 | 22 | 2 | 9.0909 | |
| ltrigg-rtg2 | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.8903 | 99.8539 | 99.9268 | 27.2049 | 2734 | 4 | 2730 | 2 | 2 | 100.0000 | |
| ltrigg-rtg2 | SNP | * | map_l150_m1_e0 | het | 98.0986 | 96.4227 | 99.8338 | 58.7339 | 18625 | 691 | 18625 | 31 | 2 | 6.4516 | |
| ltrigg-rtg2 | SNP | * | map_l150_m2_e0 | het | 98.1544 | 96.5480 | 99.8151 | 61.4966 | 19438 | 695 | 19439 | 36 | 2 | 5.5556 | |
| ltrigg-rtg2 | SNP | * | map_l150_m2_e1 | het | 98.1705 | 96.5771 | 99.8173 | 61.6528 | 19666 | 697 | 19666 | 36 | 2 | 5.5556 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 98.3095 | 98.4375 | 98.1818 | 86.2989 | 378 | 6 | 378 | 7 | 2 | 28.5714 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.3521 | 100.0000 | 98.7124 | 72.0288 | 230 | 0 | 230 | 3 | 2 | 66.6667 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | * | 94.5055 | 93.4783 | 95.5556 | 67.1533 | 43 | 3 | 43 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | map_siren | * | 93.8073 | 95.8042 | 91.8919 | 95.1823 | 137 | 6 | 136 | 12 | 2 | 16.6667 | |
| ckim-vqsr | INDEL | D16_PLUS | map_siren | het | 92.4513 | 97.4359 | 87.9518 | 96.3127 | 76 | 2 | 73 | 10 | 2 | 20.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | segdup | * | 91.8033 | 96.5517 | 87.5000 | 96.9711 | 56 | 2 | 56 | 8 | 2 | 25.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 82.7698 | 70.8758 | 99.4609 | 27.5391 | 348 | 143 | 369 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_l100_m0_e0 | het | 96.0537 | 96.7851 | 95.3333 | 90.9829 | 572 | 19 | 572 | 28 | 2 | 7.1429 | |
| ckim-vqsr | INDEL | D1_5 | map_l100_m0_e0 | homalt | 99.0329 | 99.2248 | 98.8417 | 84.1880 | 256 | 2 | 256 | 3 | 2 | 66.6667 | |
| ckim-vqsr | INDEL | D1_5 | map_l100_m1_e0 | homalt | 99.3232 | 99.1554 | 99.4915 | 83.5517 | 587 | 5 | 587 | 3 | 2 | 66.6667 | |
| ckim-vqsr | INDEL | D1_5 | map_l100_m2_e0 | homalt | 99.3443 | 99.1817 | 99.5074 | 84.1571 | 606 | 5 | 606 | 3 | 2 | 66.6667 | |
| ckim-vqsr | INDEL | D1_5 | map_l100_m2_e1 | homalt | 99.3538 | 99.1935 | 99.5146 | 84.2025 | 615 | 5 | 615 | 3 | 2 | 66.6667 | |
| ckim-vqsr | INDEL | D1_5 | map_l125_m0_e0 | homalt | 98.9899 | 99.3243 | 98.6577 | 87.4685 | 147 | 1 | 147 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_l125_m1_e0 | homalt | 99.2826 | 99.1404 | 99.4253 | 85.7785 | 346 | 3 | 346 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_l125_m2_e0 | homalt | 99.3122 | 99.1758 | 99.4490 | 86.4855 | 361 | 3 | 361 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_l125_m2_e1 | homalt | 99.3271 | 99.1935 | 99.4609 | 86.4599 | 369 | 3 | 369 | 2 | 2 | 100.0000 | |