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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
56151-56200 / 86044 show all | |||||||||||||||
| egarrison-hhga | INDEL | * | map_l150_m2_e0 | * | 97.7239 | 97.5142 | 97.9345 | 98.6965 | 1373 | 35 | 1375 | 29 | 10 | 34.4828 | |
| rpoplin-dv42 | INDEL | * | map_l125_m0_e0 | het | 97.2591 | 96.5928 | 97.9346 | 88.6168 | 567 | 20 | 569 | 12 | 3 | 25.0000 | |
| ndellapenna-hhga | INDEL | * | map_l150_m2_e1 | het | 97.3952 | 96.8615 | 97.9348 | 89.3740 | 895 | 29 | 901 | 19 | 5 | 26.3158 | |
| ckim-dragen | SNP | tv | func_cds | het | 98.9383 | 99.9624 | 97.9351 | 42.1131 | 2656 | 1 | 2656 | 56 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 86.4554 | 77.3846 | 97.9351 | 23.6486 | 503 | 147 | 332 | 7 | 7 | 100.0000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 89.9729 | 83.2080 | 97.9351 | 51.7094 | 332 | 67 | 332 | 7 | 4 | 57.1429 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.6078 | 97.2827 | 97.9351 | 45.4096 | 9201 | 257 | 9201 | 194 | 187 | 96.3918 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 59.5793 | 42.8121 | 97.9353 | 47.2358 | 1629 | 2176 | 3178 | 67 | 62 | 92.5373 | |
| rpoplin-dv42 | INDEL | * | map_l100_m0_e0 | * | 97.4296 | 96.9290 | 97.9355 | 98.6839 | 1515 | 48 | 1518 | 32 | 12 | 37.5000 | |
| ltrigg-rtg1 | SNP | * | segdup | het | 98.6738 | 99.4225 | 97.9363 | 87.6799 | 17217 | 100 | 17227 | 363 | 1 | 0.2755 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.9637 | 97.9911 | 97.9364 | 69.6975 | 1756 | 36 | 1756 | 37 | 31 | 83.7838 | |
| hfeng-pmm1 | SNP | * | map_l250_m0_e0 | het | 97.8398 | 97.7424 | 97.9375 | 93.0288 | 1472 | 34 | 1472 | 31 | 4 | 12.9032 | |
| hfeng-pmm2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 85.9729 | 76.6129 | 97.9381 | 89.9168 | 95 | 29 | 95 | 2 | 0 | 0.0000 | |
| hfeng-pmm3 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 91.5663 | 85.9729 | 97.9381 | 91.4197 | 190 | 31 | 190 | 4 | 0 | 0.0000 | |
| jli-custom | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 94.1243 | 90.5963 | 97.9381 | 81.4176 | 395 | 41 | 380 | 8 | 3 | 37.5000 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 93.7007 | 89.8148 | 97.9381 | 75.3181 | 97 | 11 | 95 | 2 | 1 | 50.0000 | |
| gduggal-bwafb | SNP | ti | map_l250_m0_e0 | * | 97.5073 | 97.0803 | 97.9381 | 93.5330 | 1330 | 40 | 1330 | 28 | 9 | 32.1429 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 22.9356 | 12.9887 | 97.9381 | 34.8993 | 103 | 690 | 95 | 2 | 2 | 100.0000 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.0000 | 92.2330 | 97.9381 | 88.2850 | 190 | 16 | 190 | 4 | 2 | 50.0000 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.9695 | 96.0199 | 97.9381 | 88.9898 | 193 | 8 | 190 | 4 | 1 | 25.0000 | |
| ltrigg-rtg1 | INDEL | I1_5 | map_l150_m0_e0 | het | 93.5961 | 89.6226 | 97.9381 | 82.0037 | 95 | 11 | 95 | 2 | 0 | 0.0000 | |
| astatham-gatk | INDEL | I6_15 | map_siren | * | 95.6376 | 93.4426 | 97.9381 | 85.2956 | 285 | 20 | 285 | 6 | 4 | 66.6667 | |
| bgallagher-sentieon | SNP | tv | map_l250_m0_e0 | homalt | 98.1912 | 98.4456 | 97.9381 | 92.2400 | 190 | 3 | 190 | 4 | 3 | 75.0000 | |
| jmaeng-gatk | INDEL | I16_PLUS | * | * | 97.0081 | 96.0953 | 97.9383 | 71.0190 | 6128 | 249 | 6128 | 129 | 82 | 63.5659 | |
| qzeng-custom | INDEL | * | * | homalt | 98.3570 | 98.7793 | 97.9383 | 51.6092 | 123644 | 1528 | 123655 | 2603 | 1560 | 59.9308 | |
| ckim-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.8341 | 99.7463 | 97.9383 | 44.8790 | 11404 | 29 | 11401 | 240 | 3 | 1.2500 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.5160 | 97.0969 | 97.9388 | 58.0884 | 17158 | 513 | 17153 | 361 | 342 | 94.7368 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.5160 | 97.0969 | 97.9388 | 58.0884 | 17158 | 513 | 17153 | 361 | 342 | 94.7368 | |
| cchapple-custom | INDEL | D6_15 | HG002complexvar | * | 96.6422 | 95.3791 | 97.9391 | 52.4803 | 5057 | 245 | 5085 | 107 | 98 | 91.5888 | |
| eyeh-varpipe | SNP | tv | map_l250_m2_e0 | * | 98.7380 | 99.5489 | 97.9403 | 90.6578 | 2869 | 13 | 2853 | 60 | 6 | 10.0000 | |
| cchapple-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.2858 | 94.6860 | 97.9405 | 73.0746 | 392 | 22 | 428 | 9 | 6 | 66.6667 | |
| astatham-gatk | INDEL | * | map_l125_m2_e0 | * | 96.5138 | 95.1275 | 97.9410 | 89.1008 | 2089 | 107 | 2093 | 44 | 9 | 20.4545 | |
| jli-custom | INDEL | * | map_l125_m0_e0 | het | 97.6068 | 97.2743 | 97.9417 | 88.6222 | 571 | 16 | 571 | 12 | 2 | 16.6667 | |
| ghariani-varprowl | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 98.9200 | 99.9179 | 97.9418 | 56.8515 | 6083 | 5 | 6091 | 128 | 59 | 46.0938 | |
| jmaeng-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.7300 | 99.5308 | 97.9420 | 44.2389 | 4667 | 22 | 4664 | 98 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 93.3929 | 89.2473 | 97.9424 | 67.1177 | 166 | 20 | 238 | 5 | 4 | 80.0000 | |
| ckim-vqsr | SNP | tv | map_l150_m0_e0 | * | 60.1129 | 43.3637 | 97.9437 | 94.7907 | 1810 | 2364 | 1810 | 38 | 0 | 0.0000 | |
| ckim-vqsr | SNP | ti | map_l250_m0_e0 | * | 55.0131 | 38.2482 | 97.9439 | 98.4056 | 524 | 846 | 524 | 11 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | * | HG002complexvar | het | 97.6548 | 97.3665 | 97.9448 | 54.4695 | 44995 | 1217 | 44989 | 944 | 675 | 71.5042 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.2818 | 98.6207 | 97.9452 | 69.3920 | 429 | 6 | 429 | 9 | 4 | 44.4444 | |
| ltrigg-rtg1 | INDEL | C6_15 | * | hetalt | 0.0000 | 0.0000 | 97.9452 | 93.5654 | 0 | 0 | 143 | 3 | 2 | 66.6667 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 82.6590 | 71.5000 | 97.9452 | 72.2960 | 143 | 57 | 143 | 3 | 3 | 100.0000 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.8252 | 99.7211 | 97.9452 | 60.2829 | 715 | 2 | 715 | 15 | 14 | 93.3333 | |
| raldana-dualsentieon | INDEL | I6_15 | map_siren | * | 95.8124 | 93.7705 | 97.9452 | 80.9150 | 286 | 19 | 286 | 6 | 3 | 50.0000 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.7221 | 97.5000 | 97.9452 | 89.4888 | 156 | 4 | 143 | 3 | 1 | 33.3333 | |
| gduggal-bwaplat | INDEL | I6_15 | HG002complexvar | homalt | 91.5364 | 85.9143 | 97.9458 | 60.0075 | 1043 | 171 | 1049 | 22 | 17 | 77.2727 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 49.6674 | 33.2688 | 97.9463 | 41.1847 | 1546 | 3101 | 2480 | 52 | 48 | 92.3077 | |
| bgallagher-sentieon | SNP | tv | map_l150_m2_e1 | het | 98.6417 | 99.3468 | 97.9466 | 79.9186 | 7300 | 48 | 7298 | 153 | 20 | 13.0719 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.6838 | 97.4223 | 97.9467 | 56.1751 | 36925 | 977 | 36731 | 770 | 739 | 95.9740 | |
| mlin-fermikit | INDEL | I1_5 | segdup | * | 96.3512 | 94.8064 | 97.9472 | 92.1265 | 1004 | 55 | 1002 | 21 | 17 | 80.9524 | |