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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
73701-73750 / 86044 show all | |||||||||||||||
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 72.9624 | 58.1711 | 97.8403 | 43.0063 | 1584 | 1139 | 1495 | 33 | 31 | 93.9394 | |
| egarrison-hhga | INDEL | * | map_l100_m2_e1 | het | 97.4787 | 97.9513 | 97.0105 | 84.5478 | 2295 | 48 | 2304 | 71 | 31 | 43.6620 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 63.1996 | 46.4567 | 98.8107 | 36.5459 | 3304 | 3808 | 2908 | 35 | 31 | 88.5714 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 87.7109 | 81.5789 | 94.8396 | 65.2279 | 682 | 154 | 680 | 37 | 31 | 83.7838 | |
| egarrison-hhga | SNP | * | HG002compoundhet | het | 98.5499 | 97.5455 | 99.5752 | 43.4625 | 13830 | 348 | 13830 | 59 | 31 | 52.5424 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.7529 | 94.2568 | 97.2973 | 83.7363 | 2232 | 136 | 2232 | 62 | 31 | 50.0000 | |
| egarrison-hhga | SNP | * | map_l100_m1_e0 | het | 99.3656 | 98.9352 | 99.7999 | 63.8790 | 44876 | 483 | 44877 | 90 | 31 | 34.4444 | |
| egarrison-hhga | SNP | * | map_l100_m2_e0 | het | 99.3648 | 98.9461 | 99.7870 | 65.4283 | 45910 | 489 | 45911 | 98 | 31 | 31.6327 | |
| egarrison-hhga | SNP | * | map_l100_m2_e1 | het | 99.3694 | 98.9552 | 99.7871 | 65.4429 | 46408 | 490 | 46409 | 99 | 31 | 31.3131 | |
| egarrison-hhga | SNP | ti | map_l100_m1_e0 | * | 99.5648 | 99.2719 | 99.8594 | 62.6430 | 47582 | 349 | 47583 | 67 | 31 | 46.2687 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9850 | 98.7098 | 99.2618 | 74.4815 | 14383 | 188 | 14387 | 107 | 31 | 28.9720 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9850 | 98.7098 | 99.2618 | 74.4815 | 14383 | 188 | 14387 | 107 | 31 | 28.9720 | |
| eyeh-varpipe | INDEL | * | map_l125_m1_e0 | homalt | 97.0129 | 97.1311 | 96.8950 | 86.7449 | 711 | 21 | 1061 | 34 | 31 | 91.1765 | |
| eyeh-varpipe | INDEL | * | segdup | het | 96.4604 | 95.6344 | 97.3009 | 93.4137 | 1402 | 64 | 1478 | 41 | 31 | 75.6098 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 87.8990 | 80.2937 | 97.0958 | 47.6367 | 1039 | 255 | 1237 | 37 | 31 | 83.7838 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 95.0368 | 92.4855 | 97.7328 | 30.1370 | 1600 | 130 | 1595 | 37 | 31 | 83.7838 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.9637 | 97.9911 | 97.9364 | 69.6975 | 1756 | 36 | 1756 | 37 | 31 | 83.7838 | |
| ckim-vqsr | SNP | * | map_siren | * | 85.1088 | 74.3093 | 99.5811 | 71.1680 | 108661 | 37567 | 108641 | 457 | 31 | 6.7834 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 94.2166 | 90.2898 | 98.5006 | 65.6575 | 25924 | 2788 | 26146 | 398 | 31 | 7.7889 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 94.2166 | 90.2898 | 98.5006 | 65.6575 | 25924 | 2788 | 26146 | 398 | 31 | 7.7889 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 96.8519 | 94.5071 | 99.3160 | 27.2218 | 6951 | 404 | 6970 | 48 | 31 | 64.5833 | |
| ckim-isaac | SNP | ti | * | het | 98.7325 | 97.5284 | 99.9667 | 15.6908 | 1250214 | 31683 | 1250525 | 417 | 31 | 7.4341 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.9803 | 97.1761 | 94.8136 | 51.0706 | 585 | 17 | 585 | 32 | 31 | 96.8750 | |
| hfeng-pmm3 | INDEL | I6_15 | HG002complexvar | * | 98.1740 | 97.0367 | 99.3383 | 57.2224 | 4650 | 142 | 4654 | 31 | 31 | 100.0000 | |
| hfeng-pmm3 | SNP | * | map_l100_m1_e0 | * | 99.6620 | 99.5870 | 99.7371 | 63.4436 | 72104 | 299 | 72093 | 190 | 31 | 16.3158 | |
| hfeng-pmm3 | SNP | * | map_l100_m2_e0 | * | 99.6651 | 99.5917 | 99.7386 | 65.1842 | 73662 | 302 | 73651 | 193 | 31 | 16.0622 | |
| hfeng-pmm3 | SNP | * | map_l100_m2_e1 | * | 99.6666 | 99.5946 | 99.7387 | 65.1913 | 74434 | 303 | 74423 | 195 | 31 | 15.8974 | |
| hfeng-pmm3 | SNP | tv | * | * | 99.9443 | 99.9171 | 99.9715 | 21.1004 | 968886 | 804 | 968804 | 276 | 31 | 11.2319 | |
| hfeng-pmm2 | SNP | ti | HG002complexvar | homalt | 99.9798 | 99.9757 | 99.9840 | 18.5051 | 193416 | 47 | 193407 | 31 | 31 | 100.0000 | |
| hfeng-pmm1 | SNP | ti | HG002complexvar | * | 99.8935 | 99.8000 | 99.9872 | 17.3497 | 507419 | 1017 | 507360 | 65 | 31 | 47.6923 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.1507 | 97.5083 | 94.8304 | 50.6380 | 587 | 15 | 587 | 32 | 31 | 96.8750 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7099 | 99.7098 | 99.7099 | 59.0011 | 28178 | 82 | 28181 | 82 | 31 | 37.8049 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 96.6535 | 99.7967 | 93.7023 | 60.6607 | 491 | 1 | 491 | 33 | 31 | 93.9394 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.2201 | 93.2179 | 99.4222 | 33.5409 | 6350 | 462 | 6367 | 37 | 31 | 83.7838 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.0795 | 96.5665 | 99.6406 | 67.0543 | 15525 | 552 | 15525 | 56 | 32 | 57.1429 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.0795 | 96.5665 | 99.6406 | 67.0543 | 15525 | 552 | 15525 | 56 | 32 | 57.1429 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 96.8349 | 99.1243 | 94.6488 | 66.0998 | 566 | 5 | 566 | 32 | 32 | 100.0000 | |
| jlack-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.7961 | 99.7741 | 97.8371 | 63.8462 | 35339 | 80 | 35328 | 781 | 32 | 4.0973 | |
| jlack-gatk | SNP | ti | HG002complexvar | homalt | 99.9491 | 99.9163 | 99.9819 | 18.2375 | 193301 | 162 | 193290 | 35 | 32 | 91.4286 | |
| jli-custom | INDEL | * | HG002complexvar | het | 99.4410 | 99.0457 | 99.8394 | 56.1111 | 45771 | 441 | 45384 | 73 | 32 | 43.8356 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.5170 | 99.7054 | 99.3293 | 39.8437 | 4739 | 14 | 4739 | 32 | 32 | 100.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.6415 | 99.7240 | 99.5592 | 34.7388 | 7227 | 20 | 7227 | 32 | 32 | 100.0000 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | het | 78.0662 | 93.4911 | 67.0103 | 81.9367 | 158 | 11 | 65 | 32 | 32 | 100.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.4023 | 95.4216 | 99.4669 | 60.8921 | 8024 | 385 | 8023 | 43 | 32 | 74.4186 | |
| hfeng-pmm1 | INDEL | I6_15 | HG002complexvar | homalt | 98.6168 | 99.8353 | 97.4277 | 55.0578 | 1212 | 2 | 1212 | 32 | 32 | 100.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.6744 | 99.2727 | 96.1268 | 69.7551 | 819 | 6 | 819 | 33 | 32 | 96.9697 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.6744 | 99.2727 | 96.1268 | 69.7551 | 819 | 6 | 819 | 33 | 32 | 96.9697 | |
| hfeng-pmm1 | SNP | * | HG002complexvar | homalt | 99.9818 | 99.9754 | 99.9882 | 20.0017 | 288503 | 71 | 288488 | 34 | 32 | 94.1176 | |
| hfeng-pmm1 | SNP | * | map_l100_m1_e0 | het | 99.4173 | 99.1159 | 99.7205 | 63.9471 | 44958 | 401 | 44947 | 126 | 32 | 25.3968 | |
| hfeng-pmm1 | SNP | * | map_l100_m2_e0 | het | 99.4228 | 99.1250 | 99.7224 | 65.3363 | 45993 | 406 | 45982 | 128 | 32 | 25.0000 | |