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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
33701-33750 / 86044 show all | |||||||||||||||
| ghariani-varprowl | INDEL | I1_5 | segdup | * | 91.1523 | 91.5958 | 90.7129 | 95.2994 | 970 | 89 | 967 | 99 | 67 | 67.6768 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 94.7213 | 91.5952 | 98.0684 | 63.9529 | 534 | 49 | 660 | 13 | 13 | 100.0000 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 95.3650 | 91.5952 | 99.4585 | 65.4829 | 534 | 49 | 551 | 3 | 2 | 66.6667 | |
| ckim-vqsr | INDEL | I1_5 | * | hetalt | 95.5907 | 91.5945 | 99.9516 | 60.1444 | 10254 | 941 | 10316 | 5 | 5 | 100.0000 | |
| anovak-vg | INDEL | * | func_cds | homalt | 87.7119 | 91.5929 | 84.1463 | 33.8710 | 207 | 19 | 207 | 39 | 35 | 89.7436 | |
| gduggal-bwaplat | INDEL | * | func_cds | homalt | 95.3917 | 91.5929 | 99.5192 | 34.3849 | 207 | 19 | 207 | 1 | 1 | 100.0000 | |
| gduggal-snapfb | SNP | ti | map_l250_m2_e1 | homalt | 95.4425 | 91.5914 | 99.6317 | 92.4268 | 1623 | 149 | 1623 | 6 | 5 | 83.3333 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 86.1189 | 91.5878 | 81.2663 | 80.6056 | 871 | 80 | 937 | 216 | 179 | 82.8704 | |
| ltrigg-rtg2 | SNP | * | map_l250_m1_e0 | het | 95.5463 | 91.5878 | 99.8624 | 74.1983 | 4355 | 400 | 4355 | 6 | 1 | 16.6667 | |
| ghariani-varprowl | INDEL | I1_5 | * | homalt | 94.4302 | 91.5834 | 97.4597 | 39.6857 | 55342 | 5086 | 55284 | 1441 | 928 | 64.3997 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.9412 | 91.5789 | 96.4286 | 90.0119 | 87 | 8 | 81 | 3 | 0 | 0.0000 | |
| ltrigg-rtg1 | INDEL | * | map_l150_m1_e0 | het | 95.1397 | 91.5789 | 98.9886 | 81.0946 | 783 | 72 | 783 | 8 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.9412 | 91.5789 | 96.4286 | 90.1869 | 87 | 8 | 81 | 3 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.4891 | 91.5789 | 97.5904 | 89.8284 | 87 | 8 | 81 | 2 | 0 | 0.0000 | |
| gduggal-snapfb | INDEL | * | map_l150_m1_e0 | het | 92.2591 | 91.5789 | 92.9495 | 86.7487 | 783 | 72 | 791 | 60 | 12 | 20.0000 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.9873 | 91.5781 | 96.5267 | 61.0569 | 1207 | 111 | 1195 | 43 | 42 | 97.6744 | |
| gduggal-snapfb | INDEL | * | map_l100_m0_e0 | het | 92.0855 | 91.5769 | 92.5998 | 82.0643 | 935 | 86 | 951 | 76 | 13 | 17.1053 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 93.8883 | 91.5760 | 96.3203 | 46.9726 | 29297 | 2695 | 34055 | 1301 | 1239 | 95.2344 | |
| anovak-vg | SNP | tv | map_l125_m2_e1 | het | 77.4408 | 91.5759 | 67.0858 | 78.0971 | 9664 | 889 | 9657 | 4738 | 1048 | 22.1190 | |
| gduggal-snapplat | SNP | tv | map_l150_m2_e0 | het | 91.9870 | 91.5747 | 92.4029 | 88.3430 | 6641 | 611 | 6641 | 546 | 288 | 52.7473 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 94.7674 | 91.5730 | 98.1928 | 70.8260 | 163 | 15 | 163 | 3 | 2 | 66.6667 | |
| ckim-dragen | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.0437 | 91.5730 | 98.7879 | 71.6007 | 163 | 15 | 163 | 2 | 1 | 50.0000 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 92.3310 | 91.5713 | 93.1034 | 71.6850 | 880 | 81 | 837 | 62 | 57 | 91.9355 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 94.5966 | 91.5686 | 97.8316 | 84.9216 | 1401 | 129 | 1534 | 34 | 25 | 73.5294 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 94.5966 | 91.5686 | 97.8316 | 84.9216 | 1401 | 129 | 1534 | 34 | 25 | 73.5294 | |
| eyeh-varpipe | INDEL | I6_15 | segdup | het | 92.1647 | 91.5663 | 92.7711 | 88.6612 | 76 | 7 | 77 | 6 | 6 | 100.0000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.2602 | 91.5616 | 97.1227 | 66.9273 | 9223 | 850 | 9080 | 269 | 224 | 83.2714 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 92.9425 | 91.5612 | 94.3662 | 39.3162 | 217 | 20 | 67 | 4 | 4 | 100.0000 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 95.1902 | 91.5599 | 99.1202 | 67.5348 | 10577 | 975 | 10478 | 93 | 44 | 47.3118 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 95.1902 | 91.5599 | 99.1202 | 67.5348 | 10577 | 975 | 10478 | 93 | 44 | 47.3118 | |
| asubramanian-gatk | INDEL | * | map_l150_m1_e0 | homalt | 95.2710 | 91.5584 | 99.2974 | 89.4045 | 423 | 39 | 424 | 3 | 1 | 33.3333 | |
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 78.7482 | 91.5528 | 69.0859 | 44.8186 | 3349 | 309 | 5978 | 2675 | 2192 | 81.9439 | |
| eyeh-varpipe | INDEL | D1_5 | HG002compoundhet | het | 84.7249 | 91.5509 | 78.8462 | 70.2988 | 1582 | 146 | 533 | 143 | 97 | 67.8322 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.4009 | 91.5493 | 97.4359 | 75.4588 | 455 | 42 | 456 | 12 | 12 | 100.0000 | |
| gduggal-bwafb | INDEL | D6_15 | map_l125_m2_e0 | het | 94.5127 | 91.5493 | 97.6744 | 86.4139 | 65 | 6 | 84 | 2 | 0 | 0.0000 | |
| gduggal-bwafb | INDEL | D6_15 | map_l125_m2_e1 | het | 94.5127 | 91.5493 | 97.6744 | 86.6460 | 65 | 6 | 84 | 2 | 0 | 0.0000 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.4009 | 91.5493 | 97.4359 | 75.4588 | 455 | 42 | 456 | 12 | 12 | 100.0000 | |
| jpowers-varprowl | INDEL | D6_15 | map_l125_m2_e0 | het | 83.3333 | 91.5493 | 76.4706 | 91.2099 | 65 | 6 | 65 | 20 | 19 | 95.0000 | |
| jpowers-varprowl | INDEL | D6_15 | map_l125_m2_e1 | het | 82.8025 | 91.5493 | 75.5814 | 91.2779 | 65 | 6 | 65 | 21 | 20 | 95.2381 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.4987 | 91.5493 | 97.6445 | 76.0021 | 455 | 42 | 456 | 11 | 11 | 100.0000 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.5968 | 91.5493 | 97.8541 | 75.8173 | 455 | 42 | 456 | 10 | 7 | 70.0000 | |
| gduggal-snapfb | INDEL | * | map_l100_m2_e0 | het | 93.1137 | 91.5475 | 94.7345 | 82.7714 | 2112 | 195 | 2159 | 120 | 22 | 18.3333 | |
| egarrison-hhga | INDEL | I6_15 | * | hetalt | 95.1738 | 91.5448 | 99.1023 | 37.9004 | 7828 | 723 | 7838 | 71 | 63 | 88.7324 | |
| gduggal-snapvard | INDEL | I1_5 | map_l150_m2_e0 | homalt | 94.8894 | 91.5423 | 98.4906 | 83.3960 | 184 | 17 | 261 | 4 | 2 | 50.0000 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 95.0878 | 91.5423 | 98.9189 | 80.1715 | 184 | 17 | 183 | 2 | 0 | 0.0000 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 92.9543 | 91.5421 | 94.4108 | 58.8410 | 5877 | 543 | 11520 | 682 | 569 | 83.4311 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 92.9543 | 91.5421 | 94.4108 | 58.8410 | 5877 | 543 | 11520 | 682 | 569 | 83.4311 | |
| jpowers-varprowl | SNP | ti | map_l250_m0_e0 | het | 90.9574 | 91.5418 | 90.3805 | 95.3348 | 855 | 79 | 855 | 91 | 17 | 18.6813 | |
| ckim-vqsr | INDEL | * | segdup | hetalt | 95.5823 | 91.5385 | 100.0000 | 94.4622 | 119 | 11 | 121 | 0 | 0 | ||
| ckim-gatk | INDEL | * | segdup | hetalt | 95.5823 | 91.5385 | 100.0000 | 94.4622 | 119 | 11 | 121 | 0 | 0 | ||