PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
11001-11050 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 95.3889 | 94.4487 | 96.3481 | 51.8879 | 1242 | 73 | 1240 | 47 | 41 | 87.2340 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 75.8784 | 82.4324 | 70.2899 | 72.7811 | 122 | 26 | 97 | 41 | 41 | 100.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.1424 | 95.1756 | 99.1922 | 62.0377 | 6017 | 305 | 6017 | 49 | 41 | 83.6735 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.1424 | 95.1756 | 99.1922 | 62.0377 | 6017 | 305 | 6017 | 49 | 41 | 83.6735 | |
| hfeng-pmm1 | SNP | * | map_l125_m1_e0 | * | 99.4583 | 99.2389 | 99.6786 | 68.9911 | 44982 | 345 | 44976 | 145 | 41 | 28.2759 | |
| hfeng-pmm1 | SNP | * | map_l125_m2_e0 | * | 99.4680 | 99.2509 | 99.6861 | 70.6559 | 46373 | 350 | 46367 | 146 | 41 | 28.0822 | |
| hfeng-pmm1 | SNP | * | map_l125_m2_e1 | * | 99.4713 | 99.2564 | 99.6872 | 70.6981 | 46851 | 351 | 46845 | 147 | 41 | 27.8912 | |
| dgrover-gatk | SNP | ti | map_l125_m1_e0 | * | 99.3758 | 99.3284 | 99.4233 | 72.4326 | 29138 | 197 | 29134 | 169 | 41 | 24.2604 | |
| egarrison-hhga | INDEL | * | map_l100_m2_e1 | * | 97.3869 | 97.1778 | 97.5968 | 97.6235 | 3650 | 106 | 3655 | 90 | 41 | 45.5556 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.0142 | 90.8795 | 95.2517 | 63.6364 | 1674 | 168 | 1665 | 83 | 41 | 49.3976 | |
| ckim-isaac | SNP | * | map_siren | * | 84.8645 | 73.7800 | 99.8686 | 51.5315 | 107887 | 38341 | 107900 | 142 | 41 | 28.8732 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 92.6472 | 93.4150 | 91.8919 | 71.8393 | 610 | 43 | 612 | 54 | 41 | 75.9259 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.3777 | 93.7799 | 97.0308 | 84.5325 | 2548 | 169 | 2549 | 78 | 41 | 52.5641 | |
| egarrison-hhga | SNP | * | map_l125_m1_e0 | * | 99.4419 | 99.0690 | 99.8177 | 68.7095 | 44905 | 422 | 44905 | 82 | 41 | 50.0000 | |
| egarrison-hhga | SNP | * | map_l125_m2_e0 | * | 99.4490 | 99.0882 | 99.8124 | 70.5171 | 46297 | 426 | 46297 | 87 | 41 | 47.1264 | |
| egarrison-hhga | SNP | * | map_l125_m2_e1 | * | 99.4493 | 99.0890 | 99.8122 | 70.5609 | 46772 | 430 | 46772 | 88 | 41 | 46.5909 | |
| eyeh-varpipe | INDEL | * | map_l150_m2_e0 | * | 96.5842 | 96.1648 | 97.0072 | 95.5563 | 1354 | 54 | 1880 | 58 | 41 | 70.6897 | |
| ckim-vqsr | INDEL | I1_5 | HG002complexvar | * | 99.3737 | 98.9030 | 99.8489 | 56.8918 | 32997 | 366 | 33042 | 50 | 41 | 82.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.8560 | 94.5289 | 99.3006 | 52.1150 | 6531 | 378 | 6531 | 46 | 41 | 89.1304 | |
| ckim-vqsr | SNP | * | * | homalt | 98.9894 | 98.0027 | 99.9961 | 17.7187 | 1156590 | 23571 | 1156567 | 45 | 41 | 91.1111 | |
| gduggal-snapvard | INDEL | D1_5 | map_l125_m0_e0 | * | 85.0206 | 95.5645 | 76.5721 | 89.6278 | 474 | 22 | 621 | 190 | 41 | 21.5789 | |
| gduggal-snapvard | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 0.0000 | 0.0000 | 28.0220 | 59.5556 | 0 | 388 | 51 | 131 | 41 | 31.2977 | |
| gduggal-snapvard | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.6868 | 98.3466 | 99.0294 | 55.2658 | 16893 | 284 | 16733 | 164 | 41 | 25.0000 | |
| gduggal-snapvard | SNP | * | map_l100_m1_e0 | homalt | 98.0408 | 96.3523 | 99.7895 | 60.4906 | 26018 | 985 | 25605 | 54 | 41 | 75.9259 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 85.9762 | 77.6671 | 96.2761 | 24.1736 | 546 | 157 | 1060 | 41 | 41 | 100.0000 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 87.5160 | 85.8216 | 89.2788 | 67.7054 | 914 | 151 | 916 | 110 | 41 | 37.2727 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 66.4101 | 59.5041 | 75.1295 | 58.0435 | 144 | 98 | 145 | 48 | 41 | 85.4167 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 41.1854 | 27.9851 | 77.9570 | 49.7297 | 150 | 386 | 145 | 41 | 41 | 100.0000 | |
| gduggal-snapvard | SNP | tv | map_l150_m0_e0 | het | 83.5823 | 96.6936 | 73.6022 | 87.1311 | 2749 | 94 | 2738 | 982 | 41 | 4.1752 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 64.2160 | 51.7316 | 84.6429 | 72.1670 | 239 | 223 | 237 | 43 | 41 | 95.3488 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | * | 18.8065 | 16.0000 | 22.8070 | 67.0520 | 12 | 63 | 13 | 44 | 41 | 93.1818 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | het | 36.5768 | 92.3077 | 22.8070 | 64.5963 | 12 | 1 | 13 | 44 | 41 | 93.1818 | |
| ghariani-varprowl | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 98.8634 | 100.0000 | 97.7524 | 37.9730 | 2738 | 0 | 2740 | 63 | 41 | 65.0794 | |
| hfeng-pmm1 | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 90.9091 | 93.3148 | 88.6243 | 46.6855 | 335 | 24 | 335 | 43 | 41 | 95.3488 | |
| gduggal-snapfb | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 97.9647 | 99.1698 | 96.7887 | 50.7481 | 6689 | 56 | 6691 | 222 | 41 | 18.4685 | |
| gduggal-snapfb | SNP | * | map_siren | homalt | 99.0661 | 98.3701 | 99.7720 | 60.7462 | 54257 | 899 | 54257 | 124 | 41 | 33.0645 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 24.7522 | 14.3959 | 88.2086 | 64.5213 | 392 | 2331 | 389 | 52 | 41 | 78.8462 | |
| gduggal-snapplat | SNP | * | map_l250_m0_e0 | het | 82.6147 | 75.6972 | 90.9236 | 97.0301 | 1140 | 366 | 1142 | 114 | 41 | 35.9649 | |
| jli-custom | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.8509 | 96.2242 | 99.5336 | 65.6849 | 8945 | 351 | 8964 | 42 | 41 | 97.6190 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.5549 | 95.7315 | 99.4491 | 28.9744 | 7715 | 344 | 7762 | 43 | 41 | 95.3488 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.5549 | 95.7315 | 99.4491 | 28.9744 | 7715 | 344 | 7762 | 43 | 41 | 95.3488 | |
| jli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.5345 | 98.6462 | 98.4232 | 60.5868 | 2696 | 37 | 2684 | 43 | 41 | 95.3488 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 64.0490 | 51.5152 | 84.6429 | 72.1393 | 238 | 224 | 237 | 43 | 41 | 95.3488 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.8670 | 96.7220 | 99.0393 | 65.6223 | 15550 | 527 | 15670 | 152 | 41 | 26.9737 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.8670 | 96.7220 | 99.0393 | 65.6223 | 15550 | 527 | 15670 | 152 | 41 | 26.9737 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9588 | 99.0919 | 98.8260 | 75.8275 | 45287 | 415 | 45287 | 538 | 41 | 7.6208 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9588 | 99.0919 | 98.8260 | 75.8275 | 45287 | 415 | 45287 | 538 | 41 | 7.6208 | |
| jmaeng-gatk | SNP | * | map_l150_m1_e0 | * | 80.0329 | 67.8918 | 97.4620 | 88.1625 | 20781 | 9828 | 20775 | 541 | 41 | 7.5786 | |
| jmaeng-gatk | SNP | * | map_l150_m2_e0 | * | 80.7195 | 68.8748 | 97.4842 | 88.8293 | 21938 | 9914 | 21932 | 566 | 41 | 7.2438 | |
| jmaeng-gatk | SNP | ti | map_l125_m1_e0 | * | 84.6118 | 74.3855 | 98.0980 | 83.7120 | 21821 | 7514 | 21817 | 423 | 41 | 9.6927 | |