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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
77301-77350 / 86044 show all | |||||||||||||||
| asubramanian-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 97.9067 | 99.3856 | 96.4712 | 41.4606 | 1941 | 12 | 1941 | 71 | 67 | 94.3662 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 80.4071 | 98.1366 | 68.1034 | 35.1955 | 158 | 3 | 158 | 74 | 67 | 90.5405 | |
| asubramanian-gatk | SNP | ti | * | het | 99.0688 | 98.2225 | 99.9298 | 21.0842 | 1259105 | 22786 | 1259055 | 884 | 67 | 7.5792 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 94.6966 | 92.5757 | 96.9171 | 59.1377 | 2232 | 179 | 2232 | 71 | 67 | 94.3662 | |
| astatham-gatk | INDEL | I16_PLUS | HG002compoundhet | homalt | 8.2192 | 100.0000 | 4.2857 | 73.3840 | 3 | 0 | 3 | 67 | 67 | 100.0000 | |
| astatham-gatk | SNP | * | * | homalt | 99.9742 | 99.9548 | 99.9936 | 17.1971 | 1179627 | 534 | 1179603 | 76 | 67 | 88.1579 | |
| ckim-gatk | INDEL | I16_PLUS | * | homalt | 97.7080 | 99.6797 | 95.8128 | 71.8495 | 1556 | 5 | 1556 | 68 | 67 | 98.5294 | |
| ckim-dragen | INDEL | D6_15 | * | het | 99.2490 | 99.4651 | 99.0338 | 63.3339 | 11530 | 62 | 11480 | 112 | 67 | 59.8214 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.8754 | 99.0250 | 98.7263 | 71.7769 | 5789 | 57 | 5736 | 74 | 67 | 90.5405 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.8754 | 99.0250 | 98.7263 | 71.7769 | 5789 | 57 | 5736 | 74 | 67 | 90.5405 | |
| ckim-dragen | INDEL | I1_5 | HG002complexvar | * | 99.5809 | 99.4065 | 99.7559 | 56.6825 | 33165 | 198 | 33105 | 81 | 67 | 82.7160 | |
| ckim-dragen | SNP | * | map_l100_m0_e0 | het | 97.6312 | 98.8022 | 96.4876 | 75.1408 | 20951 | 254 | 20960 | 763 | 67 | 8.7811 | |
| ckim-dragen | SNP | ti | map_l150_m2_e0 | * | 98.2329 | 98.8933 | 97.5811 | 78.1929 | 20285 | 227 | 20292 | 503 | 67 | 13.3201 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9656 | 98.4786 | 99.4574 | 53.6403 | 10939 | 169 | 15763 | 86 | 67 | 77.9070 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.0973 | 99.5904 | 96.6483 | 30.9022 | 1945 | 8 | 1932 | 67 | 67 | 100.0000 | |
| ckim-vqsr | INDEL | I16_PLUS | * | homalt | 97.7080 | 99.6797 | 95.8128 | 71.8495 | 1556 | 5 | 1556 | 68 | 67 | 98.5294 | |
| ckim-vqsr | INDEL | I1_5 | HG002compoundhet | het | 94.8823 | 98.1176 | 91.8536 | 86.7262 | 834 | 16 | 778 | 69 | 67 | 97.1014 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.1627 | 97.3832 | 96.9432 | 73.2443 | 6252 | 168 | 6216 | 196 | 67 | 34.1837 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.1627 | 97.3832 | 96.9432 | 73.2443 | 6252 | 168 | 6216 | 196 | 67 | 34.1837 | |
| ckim-vqsr | INDEL | D16_PLUS | HG002compoundhet | het | 88.8043 | 99.2593 | 80.3419 | 59.7015 | 402 | 3 | 282 | 69 | 67 | 97.1014 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.9120 | 98.2491 | 99.5839 | 53.4969 | 24915 | 444 | 24890 | 104 | 67 | 64.4231 | |
| jlack-gatk | SNP | * | map_l250_m2_e0 | * | 93.5078 | 97.9074 | 89.4865 | 92.8768 | 7720 | 165 | 7720 | 907 | 67 | 7.3870 | |
| jlack-gatk | SNP | tv | map_l150_m1_e0 | * | 94.3885 | 98.6712 | 90.4622 | 83.2378 | 10767 | 145 | 10765 | 1135 | 67 | 5.9031 | |
| jlack-gatk | SNP | tv | map_l150_m2_e0 | * | 94.5181 | 98.7142 | 90.6642 | 84.3431 | 11209 | 146 | 11207 | 1154 | 67 | 5.8059 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1845 | 96.8509 | 99.5553 | 39.7095 | 17684 | 575 | 17685 | 79 | 67 | 84.8101 | |
| hfeng-pmm1 | SNP | ti | * | * | 99.9548 | 99.9307 | 99.9789 | 16.7547 | 2084065 | 1446 | 2084007 | 440 | 67 | 15.2273 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 84.8790 | 77.9848 | 93.1104 | 42.5160 | 921 | 260 | 919 | 68 | 68 | 100.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | * | * | 97.5778 | 96.8750 | 98.2909 | 66.6166 | 6572 | 212 | 6556 | 114 | 68 | 59.6491 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.8438 | 95.8592 | 97.8488 | 71.3186 | 4792 | 207 | 4776 | 105 | 68 | 64.7619 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.8438 | 95.8592 | 97.8488 | 71.3186 | 4792 | 207 | 4776 | 105 | 68 | 64.7619 | |
| jlack-gatk | SNP | ti | map_l150_m0_e0 | * | 94.8167 | 98.1046 | 91.7420 | 86.3569 | 7712 | 149 | 7710 | 694 | 68 | 9.7983 | |
| jlack-gatk | SNP | tv | map_l100_m0_e0 | * | 94.2911 | 98.7279 | 90.2359 | 79.7630 | 10943 | 141 | 10942 | 1184 | 68 | 5.7432 | |
| jlack-gatk | SNP | tv | map_l150_m2_e1 | * | 94.5415 | 98.7220 | 90.7006 | 84.3649 | 11355 | 147 | 11353 | 1164 | 68 | 5.8419 | |
| mlin-fermikit | INDEL | I1_5 | map_l100_m2_e0 | * | 72.7673 | 60.4532 | 91.3812 | 78.4780 | 827 | 541 | 827 | 78 | 68 | 87.1795 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 67.5878 | 77.1812 | 60.1156 | 69.6491 | 115 | 34 | 104 | 69 | 68 | 98.5507 | |
| qzeng-custom | SNP | * | map_l100_m0_e0 | homalt | 82.4060 | 70.4991 | 99.1522 | 62.7863 | 8192 | 3428 | 8070 | 69 | 68 | 98.5507 | |
| qzeng-custom | SNP | * | segdup | * | 98.6778 | 98.8634 | 98.4928 | 92.2719 | 27748 | 319 | 27512 | 421 | 68 | 16.1520 | |
| qzeng-custom | INDEL | * | map_l100_m2_e0 | * | 84.2312 | 79.3934 | 89.6968 | 87.9330 | 2932 | 761 | 3787 | 435 | 68 | 15.6322 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.2211 | 97.0040 | 99.4690 | 43.1148 | 13372 | 413 | 13301 | 71 | 68 | 95.7746 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.3014 | 97.1593 | 99.4708 | 45.1343 | 14365 | 420 | 14284 | 76 | 68 | 89.4737 | |
| ltrigg-rtg2 | SNP | * | HG002complexvar | homalt | 99.9218 | 99.8676 | 99.9761 | 19.6026 | 288192 | 382 | 288118 | 69 | 68 | 98.5507 | |
| mlin-fermikit | INDEL | * | map_l100_m1_e0 | het | 74.2630 | 62.0134 | 92.5433 | 78.0056 | 1386 | 849 | 1390 | 112 | 68 | 60.7143 | |
| mlin-fermikit | INDEL | * | map_l100_m2_e0 | het | 74.8173 | 62.7655 | 92.5973 | 79.8974 | 1448 | 859 | 1451 | 116 | 68 | 58.6207 | |
| mlin-fermikit | INDEL | * | map_l125_m0_e0 | homalt | 64.5756 | 61.6197 | 67.8295 | 81.8820 | 175 | 109 | 175 | 83 | 68 | 81.9277 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 88.3125 | 86.2357 | 90.4918 | 71.6894 | 827 | 132 | 828 | 87 | 68 | 78.1609 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 95.4096 | 96.1426 | 94.6877 | 69.8615 | 1321 | 53 | 1319 | 74 | 68 | 91.8919 | |
| jpowers-varprowl | SNP | * | map_l100_m2_e0 | homalt | 99.3403 | 99.0226 | 99.6599 | 66.2832 | 27254 | 269 | 27254 | 93 | 68 | 73.1183 | |
| jpowers-varprowl | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.3288 | 99.0403 | 97.6276 | 52.2232 | 10629 | 103 | 10658 | 259 | 68 | 26.2548 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 94.0232 | 93.5508 | 94.5004 | 64.2877 | 1233 | 85 | 1220 | 71 | 68 | 95.7746 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 99.2231 | 99.8046 | 98.6484 | 46.1418 | 5107 | 10 | 5109 | 70 | 68 | 97.1429 | |