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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
79701-79750 / 86044 show all | |||||||||||||||
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 91.2721 | 93.5191 | 89.1304 | 80.4771 | 10101 | 700 | 10578 | 1290 | 640 | 49.6124 | |
| hfeng-pmm2 | INDEL | I1_5 | HG002compoundhet | * | 96.1838 | 94.3347 | 98.1069 | 65.2150 | 11656 | 700 | 11660 | 225 | 222 | 98.6667 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.3085 | 95.2111 | 99.5005 | 59.4918 | 13917 | 700 | 13943 | 70 | 38 | 54.2857 | |
| jmaeng-gatk | INDEL | I6_15 | HG002compoundhet | * | 93.8901 | 92.0123 | 95.8462 | 36.5464 | 8075 | 701 | 8076 | 350 | 348 | 99.4286 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 95.8359 | 92.4591 | 99.4688 | 63.5748 | 8595 | 701 | 8613 | 46 | 42 | 91.3043 | |
| ckim-isaac | SNP | tv | HG002compoundhet | homalt | 88.3010 | 79.3093 | 99.5923 | 36.8889 | 2687 | 701 | 2687 | 11 | 11 | 100.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.2571 | 98.0815 | 98.4334 | 52.3164 | 35890 | 702 | 35814 | 570 | 538 | 94.3860 | |
| gduggal-snapplat | INDEL | D6_15 | HG002complexvar | homalt | 52.8983 | 39.9487 | 78.2700 | 68.0162 | 467 | 702 | 371 | 103 | 66 | 64.0777 | |
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9892 | 98.4640 | 99.5201 | 68.3963 | 45000 | 702 | 45000 | 217 | 24 | 11.0599 | |
| raldana-dualsentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9892 | 98.4640 | 99.5201 | 68.3963 | 45000 | 702 | 45000 | 217 | 24 | 11.0599 | |
| ciseli-custom | INDEL | D6_15 | HG002compoundhet | het | 21.2896 | 17.8947 | 26.2741 | 51.2425 | 153 | 702 | 531 | 1490 | 935 | 62.7517 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.2445 | 96.0604 | 98.4581 | 67.5236 | 17117 | 702 | 16730 | 262 | 221 | 84.3511 | |
| jlack-gatk | INDEL | * | HG002complexvar | * | 99.2231 | 99.0863 | 99.3603 | 58.0205 | 76235 | 703 | 76113 | 490 | 357 | 72.8571 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.1088 | 97.1353 | 99.1021 | 39.2213 | 23837 | 703 | 23839 | 216 | 207 | 95.8333 | |
| gduggal-snapplat | SNP | * | HG002compoundhet | homalt | 94.8523 | 93.4799 | 96.2656 | 42.1750 | 10079 | 703 | 10002 | 388 | 273 | 70.3608 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 85.3274 | 76.4173 | 96.5895 | 46.1939 | 2278 | 703 | 2294 | 81 | 62 | 76.5432 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.3646 | 97.7617 | 98.9750 | 61.5381 | 30705 | 703 | 30705 | 318 | 294 | 92.4528 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.3646 | 97.7617 | 98.9750 | 61.5381 | 30705 | 703 | 30705 | 318 | 294 | 92.4528 | |
| anovak-vg | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 23.7087 | 15.9091 | 46.5116 | 54.5317 | 133 | 703 | 140 | 161 | 125 | 77.6398 | |
| anovak-vg | INDEL | * | segdup | * | 73.2929 | 72.4961 | 74.1075 | 94.2874 | 1853 | 703 | 1889 | 660 | 536 | 81.2121 | |
| ckim-gatk | SNP | tv | map_l150_m0_e0 | homalt | 64.0041 | 47.0633 | 100.0000 | 87.1795 | 625 | 703 | 625 | 0 | 0 | ||
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 73.3405 | 66.4921 | 81.7614 | 45.2275 | 1397 | 704 | 1309 | 292 | 281 | 96.2329 | |
| ghariani-varprowl | SNP | * | map_l100_m1_e0 | * | 98.3728 | 99.0277 | 97.7266 | 70.1377 | 71699 | 704 | 71702 | 1668 | 318 | 19.0647 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.1966 | 96.0492 | 98.3718 | 68.1010 | 17115 | 704 | 16736 | 277 | 229 | 82.6715 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 94.3169 | 89.7764 | 99.3411 | 33.3446 | 6182 | 704 | 1960 | 13 | 13 | 100.0000 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.1082 | 88.4268 | 98.3131 | 60.7196 | 5379 | 704 | 5420 | 93 | 64 | 68.8172 | |
| jli-custom | SNP | * | HG002complexvar | * | 99.9396 | 99.9065 | 99.9727 | 19.0201 | 753676 | 705 | 753565 | 206 | 91 | 44.1748 | |
| ciseli-custom | SNP | * | HG002compoundhet | homalt | 82.3846 | 93.4613 | 73.6552 | 42.1506 | 10077 | 705 | 10037 | 3590 | 971 | 27.0474 | |
| ciseli-custom | SNP | tv | map_l150_m2_e1 | homalt | 85.5896 | 82.9463 | 88.4069 | 74.3629 | 3429 | 705 | 3424 | 449 | 348 | 77.5056 | |
| cchapple-custom | SNP | tv | map_siren | * | 97.8668 | 98.4651 | 97.2758 | 62.3550 | 45225 | 705 | 45206 | 1266 | 183 | 14.4550 | |
| raldana-dualsentieon | SNP | tv | HG002complexvar | * | 99.8458 | 99.7136 | 99.9784 | 21.7224 | 245447 | 705 | 245362 | 53 | 18 | 33.9623 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 47.0936 | 38.2121 | 61.3540 | 79.0423 | 436 | 705 | 435 | 274 | 265 | 96.7153 | |
| qzeng-custom | SNP | tv | map_l125_m0_e0 | homalt | 80.6373 | 68.2575 | 98.5026 | 73.5992 | 1516 | 705 | 1513 | 23 | 23 | 100.0000 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 80.9241 | 70.7711 | 94.4782 | 66.0416 | 1707 | 705 | 1711 | 100 | 97 | 97.0000 | |
| gduggal-snapfb | INDEL | I6_15 | HG002complexvar | het | 77.1850 | 70.0212 | 85.9817 | 41.0929 | 1649 | 706 | 2067 | 337 | 317 | 94.0653 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 49.7888 | 53.3686 | 46.6591 | 94.6882 | 808 | 706 | 824 | 942 | 56 | 5.9448 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 88.5191 | 81.9668 | 96.2101 | 86.7350 | 3209 | 706 | 3224 | 127 | 53 | 41.7323 | |
| gduggal-snapvard | SNP | ti | map_l100_m2_e1 | homalt | 97.9449 | 96.1825 | 99.7730 | 62.4406 | 17788 | 706 | 17584 | 40 | 33 | 82.5000 | |
| anovak-vg | SNP | * | map_l250_m2_e0 | het | 71.8617 | 86.4074 | 61.5077 | 92.1188 | 4488 | 706 | 4455 | 2788 | 641 | 22.9914 | |
| ciseli-custom | SNP | * | map_l150_m0_e0 | homalt | 84.0715 | 82.7097 | 85.4790 | 75.1182 | 3382 | 707 | 3373 | 573 | 459 | 80.1047 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.2854 | 93.2411 | 99.5352 | 28.3262 | 9767 | 708 | 9850 | 46 | 46 | 100.0000 | |
| jpowers-varprowl | INDEL | * | map_siren | * | 91.5569 | 90.4453 | 92.6961 | 81.8403 | 6702 | 708 | 6701 | 528 | 440 | 83.3333 | |
| hfeng-pmm3 | INDEL | * | HG002compoundhet | het | 86.9738 | 82.7064 | 91.7055 | 77.8323 | 3386 | 708 | 3151 | 285 | 268 | 94.0351 | |
| mlin-fermikit | INDEL | * | map_l100_m0_e0 | * | 65.4035 | 54.7025 | 81.3093 | 79.7697 | 855 | 708 | 857 | 197 | 137 | 69.5431 | |
| ckim-vqsr | SNP | tv | map_l250_m1_e0 | homalt | 29.3121 | 17.1729 | 100.0000 | 97.3637 | 147 | 709 | 147 | 0 | 0 | ||
| anovak-vg | SNP | ti | map_l150_m0_e0 | homalt | 84.9295 | 74.3209 | 99.0709 | 76.2265 | 2052 | 709 | 2026 | 19 | 18 | 94.7368 | |
| gduggal-bwavard | SNP | * | map_l100_m1_e0 | homalt | 98.6152 | 97.3744 | 99.8881 | 60.4751 | 26294 | 709 | 25878 | 29 | 23 | 79.3103 | |
| gduggal-bwaplat | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 88.1535 | 79.4790 | 98.9534 | 72.5834 | 2746 | 709 | 2742 | 29 | 25 | 86.2069 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 18.9437 | 10.5927 | 89.5161 | 64.6724 | 84 | 709 | 111 | 13 | 9 | 69.2308 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.2751 | 93.2220 | 99.5351 | 28.3303 | 9765 | 710 | 9848 | 46 | 46 | 100.0000 | |