PrecisionFDA
Truth Challenge
Engage and improve DNA test results with our community challenges
Explore HG002 comparison results
Use this interactive explorer to filter all results across submission entries and multiple dimensions.
| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
9901-9950 / 86044 show all | |||||||||||||||
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 87.1230 | 91.0747 | 83.5000 | 78.7460 | 500 | 49 | 501 | 99 | 52 | 52.5253 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 22.4719 | 41.6667 | 15.3846 | 67.8218 | 10 | 14 | 10 | 55 | 52 | 94.5455 | |
| ghariani-varprowl | INDEL | * | map_l150_m2_e0 | * | 91.0274 | 94.3892 | 87.8968 | 95.3487 | 1329 | 79 | 1329 | 183 | 52 | 28.4153 | |
| ghariani-varprowl | INDEL | * | map_l150_m2_e1 | het | 89.8854 | 97.6190 | 83.2872 | 93.5910 | 902 | 22 | 902 | 181 | 52 | 28.7293 | |
| ghariani-varprowl | INDEL | I6_15 | map_siren | het | 79.3596 | 91.6084 | 70.0000 | 86.6760 | 131 | 12 | 133 | 57 | 52 | 91.2281 | |
| ghariani-varprowl | SNP | ti | map_l250_m1_e0 | * | 96.0095 | 97.2046 | 94.8434 | 90.8840 | 4451 | 128 | 4451 | 242 | 52 | 21.4876 | |
| ghariani-varprowl | SNP | ti | map_l250_m2_e0 | * | 96.2305 | 97.3642 | 95.1229 | 91.2925 | 4876 | 132 | 4876 | 250 | 52 | 20.8000 | |
| ghariani-varprowl | SNP | tv | map_l150_m0_e0 | het | 94.6019 | 98.6282 | 90.8914 | 86.7158 | 2804 | 39 | 2804 | 281 | 52 | 18.5053 | |
| gduggal-snapplat | INDEL | D6_15 | HG002compoundhet | hetalt | 51.7417 | 35.1859 | 97.7226 | 44.3646 | 2868 | 5283 | 2875 | 67 | 52 | 77.6119 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 29.9351 | 28.5016 | 31.5205 | 88.2158 | 525 | 1317 | 539 | 1171 | 52 | 4.4407 | |
| gduggal-snapvard | INDEL | D1_5 | map_l150_m2_e0 | het | 84.3060 | 98.2490 | 73.8286 | 91.1437 | 505 | 9 | 646 | 229 | 52 | 22.7074 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 62.5501 | 70.8661 | 55.9809 | 69.3548 | 90 | 37 | 117 | 92 | 52 | 56.5217 | |
| gduggal-snapvard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 75.3471 | 93.5728 | 63.0638 | 89.0931 | 2475 | 170 | 2433 | 1425 | 52 | 3.6491 | |
| hfeng-pmm2 | INDEL | D6_15 | HG002compoundhet | homalt | 47.5248 | 100.0000 | 31.1688 | 71.0526 | 24 | 0 | 24 | 53 | 52 | 98.1132 | |
| hfeng-pmm2 | INDEL | I16_PLUS | HG002compoundhet | * | 94.8024 | 92.3472 | 97.3917 | 52.6892 | 1979 | 164 | 1979 | 53 | 52 | 98.1132 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 97.3289 | 98.9813 | 95.7307 | 72.6231 | 1166 | 12 | 1166 | 52 | 52 | 100.0000 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.8331 | 99.2999 | 96.4089 | 78.7770 | 28511 | 201 | 28511 | 1062 | 52 | 4.8964 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.8331 | 99.2999 | 96.4089 | 78.7770 | 28511 | 201 | 28511 | 1062 | 52 | 4.8964 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 82.8877 | 86.3510 | 79.6915 | 44.5869 | 310 | 49 | 310 | 79 | 52 | 65.8228 | |
| ckim-isaac | INDEL | I6_15 | * | hetalt | 81.9509 | 69.9567 | 98.9089 | 28.8855 | 5982 | 2569 | 5983 | 66 | 52 | 78.7879 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 84.3015 | 79.4055 | 89.8409 | 68.3211 | 748 | 194 | 734 | 83 | 52 | 62.6506 | |
| egarrison-hhga | INDEL | D16_PLUS | HG002compoundhet | homalt | 16.0000 | 75.0000 | 8.9552 | 46.8254 | 6 | 2 | 6 | 61 | 52 | 85.2459 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.4707 | 98.0557 | 98.8892 | 80.4368 | 10591 | 210 | 10594 | 119 | 52 | 43.6975 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 0.0000 | 0.0000 | 65.6652 | 95.8907 | 0 | 0 | 153 | 80 | 52 | 65.0000 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 94.7466 | 91.9826 | 97.6819 | 48.8321 | 2742 | 239 | 2739 | 65 | 51 | 78.4615 | |
| egarrison-hhga | SNP | ti | HG002complexvar | het | 99.8118 | 99.6651 | 99.9589 | 16.9554 | 313712 | 1054 | 313715 | 129 | 51 | 39.5349 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.1462 | 92.9163 | 99.6087 | 28.2901 | 12789 | 975 | 12983 | 51 | 51 | 100.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.0845 | 92.7950 | 99.6157 | 30.7178 | 13021 | 1011 | 13220 | 51 | 51 | 100.0000 | |
| dgrover-gatk | SNP | ti | map_siren | het | 99.5897 | 99.6105 | 99.5689 | 58.1271 | 62139 | 243 | 62130 | 269 | 51 | 18.9591 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 71.7925 | 70.7207 | 72.8972 | 84.2415 | 157 | 65 | 156 | 58 | 51 | 87.9310 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | het | 56.0000 | 84.0000 | 42.0000 | 67.7419 | 42 | 8 | 42 | 58 | 51 | 87.9310 | |
| dgrover-gatk | INDEL | * | HG002complexvar | het | 99.6862 | 99.5586 | 99.8141 | 57.9282 | 46008 | 204 | 45634 | 85 | 51 | 60.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 92.6612 | 92.6531 | 92.6694 | 58.4244 | 681 | 54 | 670 | 53 | 51 | 96.2264 | |
| gduggal-bwavard | INDEL | * | map_l150_m2_e1 | * | 90.5345 | 95.2745 | 86.2437 | 91.9653 | 1371 | 68 | 1373 | 219 | 51 | 23.2877 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m2_e1 | * | 92.7581 | 94.9974 | 90.6219 | 86.9648 | 1842 | 97 | 1807 | 187 | 51 | 27.2727 | |
| eyeh-varpipe | SNP | * | map_l100_m1_e0 | * | 98.6894 | 99.7348 | 97.6657 | 67.8112 | 72211 | 192 | 69996 | 1673 | 51 | 3.0484 | |
| eyeh-varpipe | SNP | * | map_l100_m2_e0 | * | 98.6905 | 99.7377 | 97.6651 | 69.5065 | 73770 | 194 | 71526 | 1710 | 51 | 2.9825 | |
| eyeh-varpipe | SNP | * | map_l100_m2_e1 | * | 98.6948 | 99.7404 | 97.6710 | 69.5344 | 74543 | 194 | 72256 | 1723 | 51 | 2.9600 | |
| eyeh-varpipe | SNP | * | map_siren | het | 98.0835 | 99.7637 | 96.4589 | 61.2396 | 90776 | 215 | 87713 | 3220 | 51 | 1.5839 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.8642 | 99.2036 | 98.5271 | 69.1157 | 11460 | 92 | 11104 | 166 | 51 | 30.7229 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.8642 | 99.2036 | 98.5271 | 69.1157 | 11460 | 92 | 11104 | 166 | 51 | 30.7229 | |
| gduggal-bwafb | SNP | tv | map_l125_m2_e0 | * | 98.6658 | 98.8902 | 98.4424 | 74.7627 | 16306 | 183 | 16306 | 258 | 51 | 19.7674 | |
| gduggal-bwafb | SNP | tv | map_l125_m2_e1 | * | 98.6792 | 98.9014 | 98.4580 | 74.8361 | 16474 | 183 | 16474 | 258 | 51 | 19.7674 | |
| gduggal-bwaplat | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 78.4779 | 66.1838 | 96.3816 | 73.7433 | 1462 | 747 | 1465 | 55 | 51 | 92.7273 | |
| eyeh-varpipe | INDEL | C6_15 | * | * | 89.4022 | 100.0000 | 80.8354 | 93.6057 | 7 | 0 | 329 | 78 | 51 | 65.3846 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 55.9006 | 50.5618 | 62.5000 | 73.6264 | 90 | 88 | 90 | 54 | 51 | 94.4444 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 70.1923 | 90.1235 | 57.4803 | 74.8016 | 73 | 8 | 73 | 54 | 51 | 94.4444 | |
| gduggal-bwavard | SNP | tv | map_l150_m2_e1 | * | 94.1240 | 97.9830 | 90.5575 | 83.2923 | 11270 | 232 | 11240 | 1172 | 51 | 4.3515 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.7954 | 98.2348 | 99.3624 | 57.2660 | 16139 | 290 | 16208 | 104 | 51 | 49.0385 | |
| gduggal-bwaplat | INDEL | I16_PLUS | * | homalt | 87.5361 | 80.5253 | 95.8841 | 57.8947 | 1257 | 304 | 1258 | 54 | 51 | 94.4444 | |