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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
68001-68050 / 86044 show all | |||||||||||||||
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 75.0708 | 63.2962 | 92.2274 | 85.6453 | 795 | 461 | 795 | 67 | 11 | 16.4179 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 55.8252 | 40.8058 | 88.3408 | 90.2407 | 395 | 573 | 394 | 52 | 11 | 21.1538 | |
| gduggal-bwaplat | INDEL | * | map_l100_m2_e0 | * | 80.6607 | 68.1018 | 98.8989 | 92.5303 | 2515 | 1178 | 2515 | 28 | 11 | 39.2857 | |
| gduggal-bwaplat | INDEL | * | map_l100_m2_e1 | * | 80.6558 | 68.1044 | 98.8790 | 92.5655 | 2558 | 1198 | 2558 | 29 | 11 | 37.9310 | |
| gduggal-bwaplat | INDEL | D16_PLUS | * | hetalt | 80.2709 | 67.4599 | 99.0881 | 50.5635 | 1304 | 629 | 1304 | 12 | 11 | 91.6667 | |
| gduggal-bwaplat | INDEL | D16_PLUS | * | homalt | 89.7870 | 82.0922 | 99.0734 | 63.7561 | 1389 | 303 | 1390 | 13 | 11 | 84.6154 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 80.2465 | 67.4262 | 99.0868 | 50.5085 | 1302 | 629 | 1302 | 12 | 11 | 91.6667 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 83.0162 | 71.4904 | 98.9726 | 45.1128 | 1156 | 461 | 1156 | 12 | 11 | 91.6667 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 82.5318 | 70.7702 | 98.9822 | 46.3359 | 1167 | 482 | 1167 | 12 | 11 | 91.6667 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 80.2465 | 67.4262 | 99.0868 | 50.5085 | 1302 | 629 | 1302 | 12 | 11 | 91.6667 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 63.9582 | 52.6316 | 81.4969 | 78.9220 | 390 | 351 | 392 | 89 | 11 | 12.3596 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.8366 | 99.9727 | 99.7008 | 51.3048 | 3665 | 1 | 3665 | 11 | 11 | 100.0000 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 95.3125 | 100.0000 | 91.0448 | 86.9776 | 122 | 0 | 122 | 12 | 11 | 91.6667 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 94.9273 | 92.5764 | 97.4006 | 82.2668 | 636 | 51 | 637 | 17 | 11 | 64.7059 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.6425 | 98.1293 | 99.1611 | 76.9773 | 2413 | 46 | 2364 | 20 | 11 | 55.0000 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.1541 | 94.6964 | 99.7428 | 58.3391 | 5428 | 304 | 5429 | 14 | 11 | 78.5714 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.1487 | 97.4632 | 98.8439 | 76.5004 | 1921 | 50 | 1881 | 22 | 11 | 50.0000 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.1487 | 97.4632 | 98.8439 | 76.5004 | 1921 | 50 | 1881 | 22 | 11 | 50.0000 | |
| jmaeng-gatk | SNP | * | HG002compoundhet | homalt | 99.4551 | 99.0262 | 99.8877 | 35.0471 | 10677 | 105 | 10676 | 12 | 11 | 91.6667 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 99.1693 | 98.8590 | 99.4815 | 88.1277 | 2686 | 31 | 2686 | 14 | 11 | 78.5714 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.3451 | 99.1719 | 99.5189 | 81.7458 | 6826 | 57 | 6826 | 33 | 11 | 33.3333 | |
| jmaeng-gatk | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.7273 | 99.7114 | 99.7433 | 70.7941 | 6218 | 18 | 6218 | 16 | 11 | 68.7500 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | HG002compoundhet | hetalt | 94.9583 | 90.9232 | 99.3682 | 22.2073 | 1753 | 175 | 1730 | 11 | 11 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 92.7242 | 88.2707 | 97.6510 | 77.3039 | 587 | 78 | 582 | 14 | 11 | 78.5714 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 91.3465 | 85.0256 | 98.6826 | 42.3343 | 829 | 146 | 824 | 11 | 11 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 90.6524 | 84.2181 | 98.1513 | 37.9562 | 587 | 110 | 584 | 11 | 11 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.2631 | 94.2205 | 98.3962 | 48.3858 | 1239 | 76 | 1227 | 20 | 11 | 55.0000 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | HG002complexvar | homalt | 95.1273 | 94.1748 | 96.0993 | 53.7705 | 291 | 18 | 271 | 11 | 11 | 100.0000 | |
| ltrigg-rtg1 | INDEL | I1_5 | HG002complexvar | hetalt | 97.3210 | 95.3071 | 99.4220 | 76.8604 | 1645 | 81 | 1892 | 11 | 11 | 100.0000 | |
| jli-custom | SNP | ti | map_l100_m1_e0 | homalt | 99.7965 | 99.6548 | 99.9386 | 56.4067 | 17898 | 62 | 17898 | 11 | 11 | 100.0000 | |
| jli-custom | SNP | ti | map_l100_m2_e0 | homalt | 99.8004 | 99.6614 | 99.9398 | 59.0453 | 18247 | 62 | 18247 | 11 | 11 | 100.0000 | |
| jli-custom | SNP | ti | map_l100_m2_e1 | homalt | 99.7997 | 99.6593 | 99.9404 | 59.0260 | 18431 | 63 | 18431 | 11 | 11 | 100.0000 | |
| jli-custom | SNP | tv | HG002complexvar | homalt | 99.9542 | 99.9254 | 99.9832 | 22.8543 | 95040 | 71 | 95029 | 16 | 11 | 68.7500 | |
| jli-custom | SNP | tv | map_l250_m1_e0 | * | 97.9966 | 97.0155 | 98.9977 | 85.0101 | 2568 | 79 | 2568 | 26 | 11 | 42.3077 | |
| jmaeng-gatk | INDEL | * | map_l125_m1_e0 | * | 96.6159 | 98.1016 | 95.1746 | 90.8498 | 2067 | 40 | 2071 | 105 | 11 | 10.4762 | |
| jmaeng-gatk | INDEL | * | map_l125_m2_e0 | * | 96.6195 | 98.1330 | 95.1520 | 91.4584 | 2155 | 41 | 2159 | 110 | 11 | 10.0000 | |
| jmaeng-gatk | INDEL | * | map_l125_m2_e1 | * | 96.6186 | 98.1124 | 95.1697 | 91.5159 | 2183 | 42 | 2187 | 111 | 11 | 9.9099 | |
| jmaeng-gatk | INDEL | * | segdup | * | 96.3424 | 98.8654 | 93.9450 | 95.7742 | 2527 | 29 | 2529 | 163 | 11 | 6.7485 | |
| jpowers-varprowl | INDEL | D6_15 | map_l150_m1_e0 | * | 81.6901 | 79.4521 | 84.0580 | 91.6566 | 58 | 15 | 58 | 11 | 11 | 100.0000 | |
| jpowers-varprowl | INDEL | D6_15 | map_l150_m1_e0 | het | 86.3636 | 97.4359 | 77.5510 | 92.9191 | 38 | 1 | 38 | 11 | 11 | 100.0000 | |
| jpowers-varprowl | INDEL | D6_15 | map_l150_m2_e0 | * | 83.0189 | 80.4878 | 85.7143 | 91.6847 | 66 | 16 | 66 | 11 | 11 | 100.0000 | |
| jpowers-varprowl | INDEL | D6_15 | map_l150_m2_e0 | het | 87.1287 | 95.6522 | 80.0000 | 92.8664 | 44 | 2 | 44 | 11 | 11 | 100.0000 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 49.7306 | 39.3443 | 67.5676 | 84.2553 | 24 | 37 | 25 | 12 | 11 | 91.6667 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 72.7273 | 71.1111 | 74.4186 | 75.2874 | 32 | 13 | 32 | 11 | 11 | 100.0000 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 19.8805 | 11.8959 | 60.4651 | 91.9021 | 32 | 237 | 26 | 17 | 11 | 64.7059 | |
| jpowers-varprowl | INDEL | I1_5 | map_l150_m1_e0 | * | 93.8197 | 91.5020 | 96.2578 | 89.2801 | 463 | 43 | 463 | 18 | 11 | 61.1111 | |
| jpowers-varprowl | INDEL | I1_5 | map_l150_m2_e0 | * | 93.8735 | 91.5222 | 96.3489 | 90.4328 | 475 | 44 | 475 | 18 | 11 | 61.1111 | |
| jpowers-varprowl | INDEL | I1_5 | map_l150_m2_e1 | * | 93.8224 | 91.5254 | 96.2376 | 90.4986 | 486 | 45 | 486 | 19 | 11 | 57.8947 | |
| jpowers-varprowl | INDEL | I1_5 | segdup | homalt | 95.4644 | 93.4461 | 97.5717 | 90.6347 | 442 | 31 | 442 | 11 | 11 | 100.0000 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 77.2449 | 73.5294 | 81.3559 | 62.8931 | 50 | 18 | 48 | 11 | 11 | 100.0000 | |