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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
34051-34100 / 86044 show all | |||||||||||||||
| gduggal-snapvard | INDEL | I1_5 | map_l125_m0_e0 | homalt | 94.6345 | 91.2281 | 98.3051 | 82.6130 | 104 | 10 | 174 | 3 | 1 | 33.3333 | |
| raldana-dualsentieon | INDEL | I6_15 | map_l100_m1_e0 | * | 94.1176 | 91.2281 | 97.1963 | 82.9346 | 104 | 10 | 104 | 3 | 0 | 0.0000 | |
| jli-custom | INDEL | I6_15 | map_l100_m1_e0 | * | 94.9772 | 91.2281 | 99.0476 | 84.4214 | 104 | 10 | 104 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | map_l100_m1_e0 | * | 94.9772 | 91.2281 | 99.0476 | 85.5769 | 104 | 10 | 104 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | map_l100_m1_e0 | * | 94.9772 | 91.2281 | 99.0476 | 85.2941 | 104 | 10 | 104 | 1 | 1 | 100.0000 | |
| gduggal-snapfb | SNP | ti | map_l250_m1_e0 | homalt | 95.2567 | 91.2259 | 99.6601 | 92.2128 | 1466 | 141 | 1466 | 5 | 4 | 80.0000 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 95.3063 | 91.2223 | 99.7730 | 55.8289 | 10538 | 1014 | 10551 | 24 | 18 | 75.0000 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 95.3063 | 91.2223 | 99.7730 | 55.8289 | 10538 | 1014 | 10551 | 24 | 18 | 75.0000 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.4582 | 91.2192 | 93.7313 | 49.9720 | 2514 | 242 | 2512 | 168 | 168 | 100.0000 | |
| gduggal-snapplat | SNP | tv | map_l125_m2_e0 | * | 93.3644 | 91.2184 | 95.6138 | 83.0664 | 15041 | 1448 | 15041 | 690 | 359 | 52.0290 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 93.1550 | 91.2173 | 95.1768 | 58.7259 | 592 | 57 | 592 | 30 | 23 | 76.6667 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 91.4286 | 91.2173 | 91.6409 | 57.2469 | 592 | 57 | 592 | 54 | 52 | 96.2963 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 72.7050 | 91.2162 | 60.4396 | 74.6165 | 135 | 13 | 110 | 72 | 71 | 98.6111 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 75.5642 | 91.2162 | 64.4970 | 75.8226 | 135 | 13 | 109 | 60 | 59 | 98.3333 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 72.4655 | 91.2162 | 60.1093 | 74.5125 | 135 | 13 | 110 | 73 | 72 | 98.6301 | |
| bgallagher-sentieon | INDEL | I6_15 | HG002compoundhet | hetalt | 95.3997 | 91.2147 | 99.9872 | 29.5092 | 7787 | 750 | 7827 | 1 | 1 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | HG002complexvar | hetalt | 93.3550 | 91.2142 | 95.5988 | 55.5303 | 924 | 89 | 934 | 43 | 43 | 100.0000 | |
| ckim-dragen | INDEL | D6_15 | HG002complexvar | hetalt | 93.7506 | 91.2142 | 96.4321 | 47.8822 | 924 | 89 | 973 | 36 | 36 | 100.0000 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 88.8749 | 91.2134 | 86.6534 | 76.1180 | 436 | 42 | 435 | 67 | 12 | 17.9104 | |
| ltrigg-rtg1 | INDEL | * | HG002compoundhet | hetalt | 95.2514 | 91.2113 | 99.6659 | 56.7239 | 22967 | 2213 | 22971 | 77 | 76 | 98.7013 | |
| hfeng-pmm1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.1927 | 91.2096 | 99.5395 | 87.2592 | 1297 | 125 | 1297 | 6 | 4 | 66.6667 | |
| gduggal-snapfb | INDEL | * | map_l100_m2_e1 | het | 92.9455 | 91.2079 | 94.7505 | 82.9512 | 2137 | 206 | 2184 | 121 | 22 | 18.1818 | |
| anovak-vg | SNP | tv | map_siren | * | 87.1130 | 91.2040 | 83.3733 | 62.1288 | 41890 | 4040 | 41755 | 8327 | 1807 | 21.7005 | |
| ghariani-varprowl | INDEL | D1_5 | HG002compoundhet | het | 36.0201 | 91.2037 | 22.4416 | 71.2332 | 1576 | 152 | 1614 | 5578 | 5463 | 97.9383 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 85.5315 | 91.2031 | 80.5239 | 75.2676 | 705 | 68 | 707 | 171 | 82 | 47.9532 | |
| gduggal-snapvard | INDEL | I1_5 | map_l125_m2_e0 | homalt | 94.9724 | 91.2023 | 99.0676 | 78.9189 | 311 | 30 | 425 | 4 | 2 | 50.0000 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 90.2515 | 91.2014 | 89.3212 | 56.4841 | 1078 | 104 | 1079 | 129 | 86 | 66.6667 | |
| dgrover-gatk | INDEL | * | map_l100_m2_e0 | hetalt | 95.0068 | 91.2000 | 99.1453 | 87.6190 | 114 | 11 | 116 | 1 | 0 | 0.0000 | |
| astatham-gatk | INDEL | * | map_l100_m2_e0 | hetalt | 95.3975 | 91.2000 | 100.0000 | 87.4865 | 114 | 11 | 116 | 0 | 0 | ||
| asubramanian-gatk | INDEL | * | map_l100_m2_e0 | hetalt | 94.6259 | 91.2000 | 98.3193 | 88.0762 | 114 | 11 | 117 | 2 | 1 | 50.0000 | |
| bgallagher-sentieon | INDEL | * | map_l100_m2_e0 | hetalt | 95.0068 | 91.2000 | 99.1453 | 86.4111 | 114 | 11 | 116 | 1 | 0 | 0.0000 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 88.5672 | 91.1998 | 86.0824 | 76.7383 | 17856 | 1723 | 18339 | 2965 | 857 | 28.9039 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 88.5672 | 91.1998 | 86.0824 | 76.7383 | 17856 | 1723 | 18339 | 2965 | 857 | 28.9039 | |
| ltrigg-rtg1 | INDEL | * | * | hetalt | 95.1862 | 91.1955 | 99.5422 | 68.0582 | 23015 | 2222 | 23702 | 109 | 107 | 98.1651 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 95.2997 | 91.1929 | 99.7939 | 58.4384 | 15480 | 1495 | 15495 | 32 | 23 | 71.8750 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 95.2997 | 91.1929 | 99.7939 | 58.4384 | 15480 | 1495 | 15495 | 32 | 23 | 71.8750 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.8440 | 91.1898 | 98.8034 | 58.6110 | 3633 | 351 | 3633 | 44 | 35 | 79.5455 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 86.9733 | 91.1887 | 83.1303 | 79.6742 | 28398 | 2744 | 28182 | 5719 | 224 | 3.9168 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 86.9733 | 91.1887 | 83.1303 | 79.6742 | 28398 | 2744 | 28182 | 5719 | 224 | 3.9168 | |
| jlack-gatk | INDEL | * | HG002complexvar | hetalt | 94.5505 | 91.1868 | 98.1719 | 68.2876 | 3373 | 326 | 3598 | 67 | 62 | 92.5373 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 93.9690 | 91.1857 | 96.9275 | 72.3266 | 14204 | 1373 | 12524 | 397 | 332 | 83.6272 | |
| gduggal-snapfb | INDEL | I1_5 | HG002compoundhet | homalt | 37.2562 | 91.1854 | 23.4106 | 77.1726 | 300 | 29 | 313 | 1024 | 936 | 91.4062 | |
| hfeng-pmm1 | INDEL | D6_15 | map_l100_m1_e0 | hetalt | 95.3846 | 91.1765 | 100.0000 | 73.5043 | 62 | 6 | 62 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | D6_15 | map_l100_m2_e0 | hetalt | 95.3846 | 91.1765 | 100.0000 | 75.0000 | 62 | 6 | 62 | 0 | 0 | ||
| gduggal-snapvard | INDEL | I1_5 | map_l150_m2_e1 | homalt | 94.7029 | 91.1765 | 98.5130 | 83.5474 | 186 | 18 | 265 | 4 | 2 | 50.0000 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 75.4613 | 91.1765 | 64.3669 | 39.3284 | 775 | 75 | 849 | 470 | 455 | 96.8085 | |
| ckim-isaac | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.1004 | 91.1765 | 99.3772 | 49.3237 | 1116 | 108 | 1117 | 7 | 6 | 85.7143 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 93.9394 | 91.1765 | 96.8750 | 67.6768 | 62 | 6 | 62 | 2 | 1 | 50.0000 | |
| cchapple-custom | INDEL | D6_15 | map_l125_m1_e0 | homalt | 93.9394 | 91.1765 | 96.8750 | 85.4545 | 31 | 3 | 31 | 1 | 1 | 100.0000 | |
| ckim-dragen | INDEL | D6_15 | map_l100_m1_e0 | hetalt | 95.3846 | 91.1765 | 100.0000 | 69.7561 | 62 | 6 | 62 | 0 | 0 | ||