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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
59001-59050 / 86044 show all | |||||||||||||||
| ltrigg-rtg2 | SNP | ti | HG002complexvar | hetalt | 99.0419 | 99.5169 | 98.5714 | 37.5000 | 206 | 1 | 207 | 3 | 3 | 100.0000 | |
| ltrigg-rtg1 | SNP | ti | HG002complexvar | hetalt | 99.0419 | 99.5169 | 98.5714 | 36.3636 | 206 | 1 | 207 | 3 | 3 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 95.3553 | 92.3423 | 98.5714 | 56.3410 | 205 | 17 | 207 | 3 | 1 | 33.3333 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 97.8578 | 97.1545 | 98.5714 | 57.5022 | 478 | 14 | 483 | 7 | 5 | 71.4286 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 95.8333 | 93.2432 | 98.5714 | 81.3830 | 69 | 5 | 69 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 96.4276 | 94.3750 | 98.5714 | 88.7910 | 151 | 9 | 138 | 2 | 0 | 0.0000 | |
| dgrover-gatk | SNP | tv | map_l125_m0_e0 | * | 98.7276 | 98.8840 | 98.5716 | 78.3574 | 6557 | 74 | 6556 | 95 | 18 | 18.9474 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 87.7042 | 78.9949 | 98.5719 | 61.4567 | 2971 | 790 | 2968 | 43 | 28 | 65.1163 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 87.7042 | 78.9949 | 98.5719 | 61.4567 | 2971 | 790 | 2968 | 43 | 28 | 65.1163 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.4316 | 96.3170 | 98.5722 | 66.0922 | 1726 | 66 | 1726 | 25 | 17 | 68.0000 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 80.0966 | 67.4532 | 98.5731 | 65.2719 | 2487 | 1200 | 2487 | 36 | 21 | 58.3333 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.3865 | 92.3996 | 98.5731 | 65.0648 | 1702 | 140 | 1727 | 25 | 7 | 28.0000 | |
| anovak-vg | SNP | * | * | * | 98.4545 | 98.3357 | 98.5736 | 21.3437 | 3003796 | 50838 | 2987348 | 43227 | 18700 | 43.2600 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.4894 | 96.4286 | 98.5739 | 66.0205 | 1728 | 64 | 1728 | 25 | 17 | 68.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | map_siren | * | 97.5076 | 96.4637 | 98.5743 | 79.6096 | 491 | 18 | 484 | 7 | 1 | 14.2857 | |
| egarrison-hhga | INDEL | * | map_l150_m2_e1 | homalt | 98.4741 | 98.3740 | 98.5743 | 89.3400 | 484 | 8 | 484 | 7 | 4 | 57.1429 | |
| dgrover-gatk | INDEL | * | map_l150_m2_e1 | homalt | 98.4741 | 98.3740 | 98.5743 | 89.6632 | 484 | 8 | 484 | 7 | 4 | 57.1429 | |
| gduggal-bwafb | INDEL | I1_5 | map_l125_m2_e1 | het | 96.4880 | 94.4882 | 98.5743 | 86.6285 | 480 | 28 | 484 | 7 | 1 | 14.2857 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 95.7841 | 93.1472 | 98.5746 | 46.7673 | 14680 | 1080 | 25103 | 363 | 284 | 78.2369 | |
| eyeh-varpipe | SNP | ti | map_siren | het | 99.1597 | 99.7515 | 98.5748 | 60.2517 | 62227 | 155 | 60657 | 877 | 34 | 3.8769 | |
| raldana-dualsentieon | INDEL | * | map_l100_m2_e1 | * | 97.9928 | 97.4175 | 98.5749 | 83.4180 | 3659 | 97 | 3666 | 53 | 13 | 24.5283 | |
| jli-custom | INDEL | * | map_l150_m2_e0 | * | 98.3640 | 98.1534 | 98.5755 | 89.3077 | 1382 | 26 | 1384 | 20 | 7 | 35.0000 | |
| gduggal-bwafb | INDEL | D16_PLUS | HG002compoundhet | het | 83.1185 | 71.8519 | 98.5755 | 24.7427 | 291 | 114 | 1730 | 25 | 25 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | map_l100_m2_e0 | het | 97.4110 | 96.2722 | 98.5771 | 78.4124 | 2221 | 86 | 2217 | 32 | 4 | 12.5000 | |
| astatham-gatk | INDEL | D6_15 | HG002complexvar | * | 98.3071 | 98.0385 | 98.5771 | 58.5385 | 5198 | 104 | 5196 | 75 | 68 | 90.6667 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.0807 | 99.5893 | 98.5772 | 65.8570 | 485 | 2 | 485 | 7 | 7 | 100.0000 | |
| ndellapenna-hhga | INDEL | * | map_l150_m2_e1 | homalt | 98.5772 | 98.5772 | 98.5772 | 88.8207 | 485 | 7 | 485 | 7 | 5 | 71.4286 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.0971 | 95.6607 | 98.5772 | 82.2319 | 485 | 22 | 485 | 7 | 5 | 71.4286 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.2939 | 98.0121 | 98.5773 | 60.5225 | 15728 | 319 | 15729 | 227 | 215 | 94.7137 | |
| mlin-fermikit | SNP | tv | map_l100_m1_e0 | het | 69.7650 | 53.9859 | 98.5774 | 56.8653 | 8323 | 7094 | 8315 | 120 | 2 | 1.6667 | |
| anovak-vg | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 97.9888 | 97.4071 | 98.5775 | 24.3272 | 1390 | 37 | 1386 | 20 | 20 | 100.0000 | |
| gduggal-bwaplat | INDEL | * | HG002complexvar | het | 89.8971 | 82.6214 | 98.5779 | 61.4508 | 38181 | 8031 | 38126 | 550 | 282 | 51.2727 | |
| gduggal-snapplat | INDEL | D1_5 | map_l150_m2_e0 | homalt | 84.2469 | 73.5537 | 98.5782 | 91.9064 | 178 | 64 | 208 | 3 | 0 | 0.0000 | |
| ckim-isaac | INDEL | I1_5 | map_l125_m0_e0 | * | 79.8464 | 67.0968 | 98.5782 | 90.1356 | 208 | 102 | 208 | 3 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.7049 | 96.8468 | 98.5782 | 88.2123 | 645 | 21 | 624 | 9 | 3 | 33.3333 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.7049 | 96.8468 | 98.5782 | 88.2123 | 645 | 21 | 624 | 9 | 3 | 33.3333 | |
| ckim-vqsr | INDEL | I1_5 | map_l100_m0_e0 | homalt | 99.2840 | 100.0000 | 98.5782 | 81.2278 | 208 | 0 | 208 | 3 | 2 | 66.6667 | |
| qzeng-custom | INDEL | * | HG002complexvar | hetalt | 90.0705 | 82.9143 | 98.5786 | 66.1860 | 3067 | 632 | 1179 | 17 | 13 | 76.4706 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 67.2691 | 51.0539 | 98.5788 | 38.7173 | 872 | 836 | 763 | 11 | 9 | 81.8182 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.3602 | 96.1713 | 98.5789 | 73.8003 | 1482 | 59 | 1873 | 27 | 17 | 62.9630 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.8419 | 99.1062 | 98.5790 | 59.3072 | 7318 | 66 | 7284 | 105 | 100 | 95.2381 | |
| ckim-vqsr | SNP | * | map_l100_m0_e0 | het | 80.5244 | 68.0594 | 98.5791 | 88.0545 | 14432 | 6773 | 14431 | 208 | 2 | 0.9615 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 91.0211 | 84.5394 | 98.5791 | 36.6641 | 8049 | 1472 | 8048 | 116 | 98 | 84.4828 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l125_m1_e0 | homalt | 99.0014 | 99.4269 | 98.5795 | 85.3088 | 347 | 2 | 347 | 5 | 5 | 100.0000 | |
| gduggal-bwavard | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.4421 | 98.3051 | 98.5795 | 46.6205 | 2436 | 42 | 2429 | 35 | 6 | 17.1429 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.8985 | 99.2195 | 98.5796 | 63.0301 | 15637 | 123 | 15477 | 223 | 202 | 90.5830 | |
| rpoplin-dv42 | INDEL | * | map_l150_m2_e1 | homalt | 98.6802 | 98.7805 | 98.5801 | 89.0274 | 486 | 6 | 486 | 7 | 6 | 85.7143 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 90.0602 | 82.8959 | 98.5801 | 34.3105 | 979 | 202 | 972 | 14 | 13 | 92.8571 | |
| anovak-vg | SNP | tv | segdup | homalt | 98.7340 | 98.8882 | 98.5802 | 89.2441 | 3202 | 36 | 3194 | 46 | 38 | 82.6087 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 90.7836 | 84.1298 | 98.5804 | 37.3201 | 2359 | 445 | 2361 | 34 | 27 | 79.4118 | |