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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
26101-26150 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | D16_PLUS | HG002compoundhet | hetalt | 96.8969 | 94.3465 | 99.5891 | 25.8850 | 1819 | 109 | 1939 | 8 | 8 | 100.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.7052 | 90.8178 | 98.9404 | 37.4482 | 633 | 64 | 747 | 8 | 8 | 100.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.9022 | 98.6444 | 99.1614 | 72.9208 | 946 | 13 | 946 | 8 | 6 | 75.0000 | |
| 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_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.3918 | 87.9802 | 99.5128 | 30.5121 | 1603 | 219 | 1634 | 8 | 8 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 97.7615 | 97.6623 | 97.8610 | 79.2798 | 376 | 9 | 366 | 8 | 7 | 87.5000 | |
| ckim-vqsr | INDEL | D1_5 | segdup | het | 98.9178 | 98.9884 | 98.8473 | 96.6564 | 685 | 7 | 686 | 8 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 93.4541 | 88.1148 | 99.4822 | 29.4843 | 1505 | 203 | 1537 | 8 | 8 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.2798 | 99.1742 | 99.3856 | 72.8070 | 1321 | 11 | 1294 | 8 | 6 | 75.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.2934 | 99.0605 | 99.5275 | 75.3924 | 1687 | 16 | 1685 | 8 | 3 | 37.5000 | |
| ckim-vqsr | INDEL | I1_5 | map_l150_m0_e0 | het | 92.9577 | 93.3962 | 92.5234 | 96.0647 | 99 | 7 | 99 | 8 | 0 | 0.0000 | |
| ckim-vqsr | SNP | * | HG002compoundhet | homalt | 98.6617 | 97.4309 | 99.9239 | 35.4419 | 10505 | 277 | 10504 | 8 | 7 | 87.5000 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.6636 | 99.5017 | 99.8260 | 39.5847 | 4593 | 23 | 4589 | 8 | 3 | 37.5000 | |
| ckim-vqsr | SNP | * | segdup | homalt | 98.5850 | 97.2820 | 99.9235 | 88.7282 | 10451 | 292 | 10451 | 8 | 8 | 100.0000 | |
| egarrison-hhga | INDEL | I1_5 | map_siren | homalt | 99.3814 | 99.4224 | 99.3405 | 78.4317 | 1205 | 7 | 1205 | 8 | 4 | 50.0000 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 88.5478 | 83.8926 | 93.7500 | 74.1935 | 125 | 24 | 120 | 8 | 6 | 75.0000 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 86.2075 | 77.4105 | 97.2603 | 45.7249 | 281 | 82 | 284 | 8 | 8 | 100.0000 | |
| egarrison-hhga | SNP | * | * | hetalt | 99.1394 | 99.1963 | 99.0826 | 48.4024 | 864 | 7 | 864 | 8 | 8 | 100.0000 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6125 | 99.4327 | 99.7930 | 57.8718 | 3856 | 22 | 3856 | 8 | 3 | 37.5000 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.2374 | 91.8182 | 92.6606 | 88.8205 | 101 | 9 | 101 | 8 | 8 | 100.0000 | |
| egarrison-hhga | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.7945 | 99.7208 | 99.8684 | 54.9696 | 6071 | 17 | 6072 | 8 | 7 | 87.5000 | |
| egarrison-hhga | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.6106 | 99.4231 | 99.7987 | 35.5602 | 3964 | 23 | 3966 | 8 | 6 | 75.0000 | |
| egarrison-hhga | SNP | ti | map_l125_m1_e0 | homalt | 99.8187 | 99.7103 | 99.9274 | 66.0474 | 11013 | 32 | 11013 | 8 | 8 | 100.0000 | |
| egarrison-hhga | SNP | ti | map_l125_m2_e0 | homalt | 99.8237 | 99.7183 | 99.9294 | 68.6664 | 11326 | 32 | 11326 | 8 | 8 | 100.0000 | |
| egarrison-hhga | SNP | ti | map_l125_m2_e1 | homalt | 99.8253 | 99.7207 | 99.9300 | 68.7014 | 11426 | 32 | 11426 | 8 | 8 | 100.0000 | |
| egarrison-hhga | SNP | tv | * | hetalt | 99.1394 | 99.1963 | 99.0826 | 48.4024 | 864 | 7 | 864 | 8 | 8 | 100.0000 | |
| eyeh-varpipe | INDEL | C16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 38.4615 | 92.2156 | 0 | 0 | 5 | 8 | 6 | 75.0000 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 0.0000 | 0.0000 | 63.6364 | 94.3590 | 0 | 0 | 14 | 8 | 2 | 25.0000 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 0.0000 | 0.0000 | 93.7008 | 92.4584 | 0 | 0 | 119 | 8 | 7 | 87.5000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 86.1862 | 76.5690 | 98.5663 | 43.2350 | 549 | 168 | 550 | 8 | 5 | 62.5000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | * | 85.5172 | 82.6667 | 88.5714 | 44.4444 | 62 | 13 | 62 | 8 | 5 | 62.5000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | het | 69.3642 | 92.3077 | 55.5556 | 70.4918 | 12 | 1 | 10 | 8 | 5 | 62.5000 | |
| ckim-isaac | INDEL | D1_5 | segdup | * | 98.5851 | 97.9148 | 99.2647 | 92.9825 | 1080 | 23 | 1080 | 8 | 3 | 37.5000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 93.0003 | 88.7701 | 97.6540 | 47.5385 | 332 | 42 | 333 | 8 | 2 | 25.0000 | |
| ckim-isaac | INDEL | I16_PLUS | HG002compoundhet | hetalt | 65.1901 | 48.5428 | 99.2149 | 33.3115 | 1016 | 1077 | 1011 | 8 | 7 | 87.5000 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 66.2956 | 51.4563 | 93.1624 | 81.5748 | 106 | 100 | 109 | 8 | 4 | 50.0000 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 77.3091 | 63.7658 | 98.1567 | 37.9113 | 403 | 229 | 426 | 8 | 7 | 87.5000 | |
| ckim-vqsr | SNP | tv | HG002complexvar | homalt | 98.0771 | 96.2349 | 99.9913 | 23.4384 | 91530 | 3581 | 91516 | 8 | 6 | 75.0000 | |
| ckim-vqsr | SNP | tv | func_cds | * | 99.7367 | 99.6568 | 99.8166 | 38.6616 | 4356 | 15 | 4355 | 8 | 0 | 0.0000 | |
| ckim-vqsr | SNP | tv | func_cds | het | 99.7366 | 99.7742 | 99.6990 | 44.6481 | 2651 | 6 | 2650 | 8 | 0 | 0.0000 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 99.0685 | 99.0142 | 99.1228 | 89.4371 | 904 | 9 | 904 | 8 | 7 | 87.5000 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.8068 | 99.8344 | 99.7793 | 75.9360 | 3617 | 6 | 3617 | 8 | 3 | 37.5000 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 95.9027 | 95.4955 | 96.3134 | 65.1685 | 212 | 10 | 209 | 8 | 5 | 62.5000 | |
| dgrover-gatk | INDEL | D16_PLUS | HG002compoundhet | hetalt | 97.0887 | 94.7095 | 99.5904 | 26.5237 | 1826 | 102 | 1945 | 8 | 8 | 100.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.9407 | 91.2482 | 98.9446 | 37.9197 | 636 | 61 | 750 | 8 | 8 | 100.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.7562 | 99.4987 | 98.0247 | 65.4437 | 397 | 2 | 397 | 8 | 6 | 75.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0605 | 98.9572 | 99.1641 | 72.4921 | 949 | 10 | 949 | 8 | 6 | 75.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.5138 | 99.8915 | 99.1389 | 78.0222 | 921 | 1 | 921 | 8 | 3 | 37.5000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 97.6284 | 97.4026 | 97.8552 | 79.4942 | 375 | 10 | 365 | 8 | 7 | 87.5000 | |
| dgrover-gatk | INDEL | D1_5 | map_l150_m0_e0 | het | 97.0684 | 98.0198 | 96.1353 | 92.6648 | 198 | 4 | 199 | 8 | 0 | 0.0000 | |