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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
20701-20750 / 86044 show all | |||||||||||||||
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 83.6814 | 77.2332 | 91.3043 | 82.9887 | 977 | 288 | 1029 | 98 | 59 | 60.2041 | |
| jlack-gatk | INDEL | D16_PLUS | * | * | 96.2606 | 96.5065 | 96.0159 | 70.3319 | 6547 | 237 | 6531 | 271 | 163 | 60.1476 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.0559 | 96.7947 | 99.3503 | 55.8922 | 41946 | 1389 | 42206 | 276 | 166 | 60.1449 | |
| rpoplin-dv42 | SNP | ti | map_l100_m2_e1 | het | 99.3494 | 99.1473 | 99.5523 | 65.6527 | 30696 | 264 | 30688 | 138 | 83 | 60.1449 | |
| anovak-vg | INDEL | * | map_l100_m1_e0 | * | 72.2354 | 72.6157 | 71.8590 | 84.0163 | 2604 | 982 | 2671 | 1046 | 628 | 60.0382 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 77.8733 | 76.5766 | 79.2148 | 62.9281 | 340 | 104 | 343 | 90 | 54 | 60.0000 | |
| anovak-vg | INDEL | D6_15 | map_l125_m2_e0 | * | 76.3127 | 73.8095 | 78.9916 | 88.9713 | 93 | 33 | 94 | 25 | 15 | 60.0000 | |
| anovak-vg | INDEL | D6_15 | map_l125_m2_e1 | * | 76.3524 | 73.4375 | 79.5082 | 88.8584 | 94 | 34 | 97 | 25 | 15 | 60.0000 | |
| anovak-vg | INDEL | D6_15 | segdup | homalt | 85.5227 | 82.0000 | 89.3617 | 91.4234 | 41 | 9 | 42 | 5 | 3 | 60.0000 | |
| astatham-gatk | SNP | tv | map_l100_m1_e0 | homalt | 99.5729 | 99.2591 | 99.8887 | 59.2933 | 8976 | 67 | 8976 | 10 | 6 | 60.0000 | |
| astatham-gatk | SNP | tv | map_l100_m2_e0 | homalt | 99.5809 | 99.2728 | 99.8908 | 61.7518 | 9147 | 67 | 9147 | 10 | 6 | 60.0000 | |
| astatham-gatk | SNP | tv | map_l100_m2_e1 | homalt | 99.5848 | 99.2797 | 99.8918 | 61.7406 | 9235 | 67 | 9235 | 10 | 6 | 60.0000 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.2975 | 98.9729 | 99.6243 | 77.9307 | 1349 | 14 | 1326 | 5 | 3 | 60.0000 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6042 | 99.3980 | 99.8112 | 69.7820 | 2642 | 16 | 2643 | 5 | 3 | 60.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.8462 | 95.9514 | 97.7578 | 81.0374 | 237 | 10 | 218 | 5 | 3 | 60.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 95.7690 | 95.3020 | 96.2406 | 77.7219 | 142 | 7 | 128 | 5 | 3 | 60.0000 | |
| astatham-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 97.2405 | 95.8549 | 98.6667 | 91.1368 | 370 | 16 | 370 | 5 | 3 | 60.0000 | |
| astatham-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 96.8807 | 95.6522 | 98.1413 | 91.1948 | 264 | 12 | 264 | 5 | 3 | 60.0000 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.0751 | 96.5596 | 97.5962 | 85.4240 | 421 | 15 | 406 | 10 | 6 | 60.0000 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.1978 | 94.7154 | 97.7273 | 88.4393 | 233 | 13 | 215 | 5 | 3 | 60.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.8896 | 96.2236 | 97.5649 | 78.3480 | 637 | 25 | 601 | 15 | 9 | 60.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.3716 | 99.1196 | 99.6249 | 77.6829 | 1351 | 12 | 1328 | 5 | 3 | 60.0000 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0886 | 98.9484 | 99.2292 | 67.4228 | 3858 | 41 | 3862 | 30 | 18 | 60.0000 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 96.6396 | 95.5466 | 97.7578 | 80.8255 | 236 | 11 | 218 | 5 | 3 | 60.0000 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 95.4289 | 94.6309 | 96.2406 | 77.3424 | 141 | 8 | 128 | 5 | 3 | 60.0000 | |
| bgallagher-sentieon | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.9202 | 99.9202 | 99.9202 | 44.4375 | 6263 | 5 | 6263 | 5 | 3 | 60.0000 | |
| anovak-vg | INDEL | I6_15 | func_cds | het | 56.0784 | 45.8333 | 72.2222 | 40.0000 | 11 | 13 | 13 | 5 | 3 | 60.0000 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 62.2222 | 66.6667 | 58.3333 | 94.7368 | 6 | 3 | 7 | 5 | 3 | 60.0000 | |
| anovak-vg | SNP | tv | map_l250_m1_e0 | homalt | 81.8115 | 69.6262 | 99.1667 | 88.3586 | 596 | 260 | 595 | 5 | 3 | 60.0000 | |
| astatham-gatk | INDEL | * | map_l100_m1_e0 | homalt | 99.3081 | 99.4295 | 99.1870 | 83.8625 | 1220 | 7 | 1220 | 10 | 6 | 60.0000 | |
| astatham-gatk | INDEL | * | map_l150_m1_e0 | homalt | 99.0270 | 99.1342 | 98.9201 | 88.5254 | 458 | 4 | 458 | 5 | 3 | 60.0000 | |
| astatham-gatk | INDEL | * | map_l150_m2_e0 | homalt | 99.0654 | 99.1684 | 98.9627 | 89.4829 | 477 | 4 | 477 | 5 | 3 | 60.0000 | |
| asubramanian-gatk | INDEL | D1_5 | HG002complexvar | het | 99.2391 | 98.6082 | 99.8781 | 56.4759 | 20476 | 289 | 20484 | 25 | 15 | 60.0000 | |
| asubramanian-gatk | INDEL | D1_5 | map_siren | homalt | 97.6001 | 95.7192 | 99.5563 | 81.8284 | 1118 | 50 | 1122 | 5 | 3 | 60.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 91.2281 | 100.0000 | 83.8710 | 92.0716 | 25 | 0 | 26 | 5 | 3 | 60.0000 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.1530 | 98.6794 | 99.6313 | 77.5757 | 1345 | 18 | 1351 | 5 | 3 | 60.0000 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.3618 | 90.6883 | 96.1977 | 79.5490 | 224 | 23 | 253 | 10 | 6 | 60.0000 | |
| asubramanian-gatk | INDEL | I6_15 | map_siren | * | 94.0200 | 90.1639 | 98.2206 | 86.0753 | 275 | 30 | 276 | 5 | 3 | 60.0000 | |
| asubramanian-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | * | 92.9792 | 91.0891 | 94.9495 | 93.3557 | 92 | 9 | 94 | 5 | 3 | 60.0000 | |
| rpoplin-dv42 | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.7460 | 99.8094 | 99.6827 | 70.4841 | 3142 | 6 | 3142 | 10 | 6 | 60.0000 | |
| rpoplin-dv42 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 99.2965 | 99.2968 | 99.2963 | 87.3102 | 1412 | 10 | 1411 | 10 | 6 | 60.0000 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 76.3948 | 71.7742 | 81.6514 | 99.9459 | 89 | 35 | 89 | 20 | 12 | 60.0000 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 98.6796 | 98.9777 | 98.3834 | 43.8974 | 2130 | 22 | 2130 | 35 | 21 | 60.0000 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 97.4626 | 97.6139 | 97.3118 | 72.5745 | 900 | 22 | 905 | 25 | 15 | 60.0000 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | homalt | 70.5882 | 100.0000 | 54.5455 | 99.5554 | 6 | 0 | 6 | 5 | 3 | 60.0000 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 88.3102 | 87.5375 | 89.0966 | 84.7216 | 583 | 83 | 572 | 70 | 42 | 60.0000 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 88.3102 | 87.5375 | 89.0966 | 84.7216 | 583 | 83 | 572 | 70 | 42 | 60.0000 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 88.8889 | 97.7778 | 81.4815 | 79.3103 | 44 | 1 | 44 | 10 | 6 | 60.0000 | |
| ndellapenna-hhga | INDEL | I1_5 | map_l100_m2_e1 | homalt | 99.0741 | 99.0741 | 99.0741 | 82.5186 | 535 | 5 | 535 | 5 | 3 | 60.0000 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 90.6589 | 89.8785 | 91.4530 | 77.6930 | 222 | 25 | 214 | 20 | 12 | 60.0000 | |