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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
51951-52000 / 86044 show all | |||||||||||||||
| dgrover-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.9009 | 99.8415 | 99.9603 | 61.7282 | 10081 | 16 | 10081 | 4 | 4 | 100.0000 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.2837 | 99.7301 | 96.8787 | 61.7262 | 11453 | 31 | 11453 | 369 | 356 | 96.4770 | |
| jlack-gatk | INDEL | * | * | het | 98.8624 | 99.4076 | 98.3232 | 61.7242 | 192983 | 1150 | 192623 | 3285 | 1088 | 33.1202 | |
| ndellapenna-hhga | SNP | * | map_l100_m1_e0 | * | 99.3352 | 98.8536 | 99.8215 | 61.7229 | 71573 | 830 | 71575 | 128 | 61 | 47.6562 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 96.0000 | 92.3077 | 100.0000 | 61.7188 | 48 | 4 | 49 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.0557 | 88.2519 | 98.4127 | 61.7176 | 1878 | 250 | 1860 | 30 | 25 | 83.3333 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 75.2854 | 64.8571 | 89.7098 | 61.7172 | 681 | 369 | 680 | 78 | 71 | 91.0256 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 95.8320 | 92.1659 | 99.8018 | 61.7166 | 10647 | 905 | 10577 | 21 | 11 | 52.3810 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 95.8320 | 92.1659 | 99.8018 | 61.7166 | 10647 | 905 | 10577 | 21 | 11 | 52.3810 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 75.6717 | 93.2362 | 63.6760 | 61.7128 | 896 | 65 | 1022 | 583 | 558 | 95.7118 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.5366 | 99.0196 | 98.0583 | 61.7100 | 101 | 1 | 101 | 2 | 2 | 100.0000 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.9646 | 94.4089 | 99.6626 | 61.7069 | 5606 | 332 | 5612 | 19 | 18 | 94.7368 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 92.3980 | 87.5241 | 97.8468 | 61.7037 | 5458 | 778 | 5635 | 124 | 11 | 8.8710 | |
| egarrison-hhga | INDEL | D16_PLUS | HG002complexvar | het | 88.9628 | 83.8302 | 94.7650 | 61.7021 | 928 | 179 | 887 | 49 | 32 | 65.3061 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 96.3131 | 94.5455 | 98.1481 | 61.7021 | 52 | 3 | 53 | 1 | 1 | 100.0000 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | het | 27.2727 | 75.0000 | 16.6667 | 61.7021 | 6 | 2 | 6 | 30 | 30 | 100.0000 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 86.8494 | 93.7143 | 80.9217 | 61.7014 | 984 | 66 | 878 | 207 | 45 | 21.7391 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 24.3587 | 15.4953 | 56.9132 | 61.6995 | 183 | 998 | 177 | 134 | 97 | 72.3881 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 94.5362 | 98.9362 | 90.5109 | 61.6962 | 744 | 8 | 744 | 78 | 78 | 100.0000 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 94.4732 | 91.9834 | 97.1014 | 61.6929 | 4888 | 426 | 4891 | 146 | 111 | 76.0274 | |
| jlack-gatk | INDEL | I1_5 | * | het | 99.1970 | 99.4952 | 98.9006 | 61.6913 | 78642 | 399 | 78625 | 874 | 231 | 26.4302 | |
| jpowers-varprowl | INDEL | D1_5 | * | het | 92.8158 | 97.3223 | 88.7081 | 61.6875 | 85229 | 2345 | 85221 | 10848 | 10534 | 97.1055 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.5468 | 91.3928 | 97.9261 | 61.6841 | 9206 | 867 | 9255 | 196 | 98 | 50.0000 | |
| ckim-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.7369 | 99.5048 | 99.9701 | 61.6836 | 10047 | 50 | 10047 | 3 | 3 | 100.0000 | |
| cchapple-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.7222 | 99.4720 | 99.9738 | 61.6817 | 11491 | 61 | 11440 | 3 | 1 | 33.3333 | |
| cchapple-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.7222 | 99.4720 | 99.9738 | 61.6817 | 11491 | 61 | 11440 | 3 | 1 | 33.3333 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 81.8219 | 73.9368 | 91.5896 | 61.6810 | 3929 | 1385 | 2973 | 273 | 264 | 96.7033 | |
| asubramanian-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4224 | 98.8809 | 99.9700 | 61.6808 | 9984 | 113 | 9996 | 3 | 3 | 100.0000 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 95.0318 | 94.2197 | 95.8580 | 61.6780 | 326 | 20 | 324 | 14 | 10 | 71.4286 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.2218 | 98.8372 | 99.6094 | 61.6766 | 255 | 3 | 255 | 1 | 1 | 100.0000 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.3380 | 94.8299 | 99.9823 | 61.6765 | 5631 | 307 | 5659 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | I16_PLUS | HG002complexvar | het | 58.4929 | 47.6692 | 75.6757 | 61.6761 | 317 | 348 | 308 | 99 | 23 | 23.2323 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.0398 | 97.0909 | 99.0074 | 61.6738 | 801 | 24 | 798 | 8 | 7 | 87.5000 | |
| ltrigg-rtg2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.0398 | 97.0909 | 99.0074 | 61.6738 | 801 | 24 | 798 | 8 | 7 | 87.5000 | |
| bgallagher-sentieon | SNP | tv | map_l100_m2_e0 | homalt | 99.7827 | 99.6636 | 99.9021 | 61.6697 | 9183 | 31 | 9183 | 9 | 6 | 66.6667 | |
| ckim-dragen | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.2525 | 95.3621 | 99.2194 | 61.6689 | 8019 | 390 | 8008 | 63 | 59 | 93.6508 | |
| qzeng-custom | SNP | ti | map_l100_m0_e0 | homalt | 81.6311 | 69.2951 | 99.3106 | 61.6670 | 5387 | 2387 | 5330 | 37 | 36 | 97.2973 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 97.1162 | 97.6582 | 96.5801 | 61.6655 | 1543 | 37 | 1525 | 54 | 6 | 11.1111 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 62.4499 | 90.8511 | 47.5768 | 61.6650 | 1281 | 129 | 1286 | 1417 | 1364 | 96.2597 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.4852 | 94.1121 | 94.8613 | 61.6630 | 3021 | 189 | 3009 | 163 | 146 | 89.5706 | |
| ltrigg-rtg1 | SNP | tv | map_l125_m1_e0 | * | 99.1139 | 98.4703 | 99.7659 | 61.6627 | 15771 | 245 | 15771 | 37 | 9 | 24.3243 | |
| bgallagher-sentieon | SNP | tv | map_l100_m2_e1 | homalt | 99.7847 | 99.6667 | 99.9030 | 61.6624 | 9271 | 31 | 9271 | 9 | 6 | 66.6667 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 33.5783 | 32.0401 | 35.2715 | 61.6614 | 1949 | 4134 | 1929 | 3540 | 3386 | 95.6497 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.5775 | 93.3816 | 100.0000 | 61.6574 | 5545 | 393 | 5580 | 0 | 0 | ||
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 86.9385 | 82.2761 | 92.1610 | 61.6572 | 441 | 95 | 435 | 37 | 30 | 81.0811 | |
| ltrigg-rtg1 | SNP | ti | map_l100_m0_e0 | homalt | 99.7102 | 99.5884 | 99.8324 | 61.6545 | 7742 | 32 | 7742 | 13 | 13 | 100.0000 | |
| ltrigg-rtg2 | SNP | * | map_l150_m2_e1 | het | 98.1705 | 96.5771 | 99.8173 | 61.6528 | 19666 | 697 | 19666 | 36 | 2 | 5.5556 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.2930 | 95.5286 | 99.1239 | 61.6524 | 8033 | 376 | 8033 | 71 | 62 | 87.3239 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.3852 | 95.7925 | 99.0319 | 61.6504 | 6056 | 266 | 6342 | 62 | 53 | 85.4839 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.3852 | 95.7925 | 99.0319 | 61.6504 | 6056 | 266 | 6342 | 62 | 53 | 85.4839 | |