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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
70401-70450 / 86044 show all | |||||||||||||||
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.6644 | 98.0498 | 99.2867 | 71.5861 | 5983 | 119 | 5985 | 43 | 7 | 16.2791 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.5549 | 95.7315 | 99.4491 | 28.9744 | 7715 | 344 | 7762 | 43 | 41 | 95.3488 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.5549 | 95.7315 | 99.4491 | 28.9744 | 7715 | 344 | 7762 | 43 | 41 | 95.3488 | |
| jli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.5345 | 98.6462 | 98.4232 | 60.5868 | 2696 | 37 | 2684 | 43 | 41 | 95.3488 | |
| ltrigg-rtg1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.9606 | 99.8160 | 98.1198 | 64.2712 | 2170 | 4 | 2244 | 43 | 1 | 2.3256 | |
| ltrigg-rtg1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.3663 | 99.7116 | 97.0568 | 64.7187 | 1383 | 4 | 1418 | 43 | 1 | 2.3256 | |
| jmaeng-gatk | INDEL | D1_5 | * | hetalt | 96.3487 | 93.3431 | 99.5544 | 62.8913 | 9563 | 682 | 9606 | 43 | 43 | 100.0000 | |
| jmaeng-gatk | INDEL | D1_5 | HG002complexvar | hetalt | 92.2064 | 88.1657 | 96.6354 | 72.5869 | 1192 | 160 | 1235 | 43 | 43 | 100.0000 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 94.1029 | 98.9446 | 89.7129 | 61.3321 | 375 | 4 | 375 | 43 | 43 | 100.0000 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 71.4004 | 63.9576 | 80.8036 | 71.2821 | 181 | 102 | 181 | 43 | 31 | 72.0930 | |
| ltrigg-rtg1 | INDEL | * | HG002complexvar | homalt | 99.4013 | 98.9677 | 99.8388 | 52.4987 | 26747 | 279 | 26629 | 43 | 32 | 74.4186 | |
| jli-custom | SNP | ti | HG002compoundhet | * | 99.7826 | 99.8112 | 99.7541 | 35.5495 | 17445 | 33 | 17445 | 43 | 22 | 51.1628 | |
| jli-custom | SNP | ti | map_l150_m0_e0 | * | 98.8029 | 98.1682 | 99.4459 | 75.0426 | 7717 | 144 | 7717 | 43 | 19 | 44.1860 | |
| jmaeng-gatk | INDEL | * | map_l150_m0_e0 | het | 92.7708 | 97.3607 | 88.5942 | 95.5715 | 332 | 9 | 334 | 43 | 1 | 2.3256 | |
| rpoplin-dv42 | SNP | * | HG002compoundhet | het | 99.5408 | 99.3864 | 99.6957 | 45.1283 | 14091 | 87 | 14087 | 43 | 32 | 74.4186 | |
| rpoplin-dv42 | SNP | * | segdup | het | 99.7082 | 99.6651 | 99.7514 | 90.3344 | 17259 | 58 | 17253 | 43 | 3 | 6.9767 | |
| rpoplin-dv42 | INDEL | * | map_l100_m2_e0 | het | 97.6728 | 97.2258 | 98.1239 | 84.2550 | 2243 | 64 | 2249 | 43 | 19 | 44.1860 | |
| rpoplin-dv42 | INDEL | D1_5 | HG002compoundhet | hetalt | 96.8685 | 94.3226 | 99.5556 | 55.8683 | 9636 | 580 | 9632 | 43 | 42 | 97.6744 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 87.2658 | 91.9890 | 83.0040 | 81.7064 | 333 | 29 | 210 | 43 | 42 | 97.6744 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 74.0331 | 94.3662 | 60.9091 | 53.7815 | 67 | 4 | 67 | 43 | 43 | 100.0000 | |
| rpoplin-dv42 | SNP | tv | map_l250_m2_e0 | het | 97.8098 | 97.8351 | 97.7846 | 87.2638 | 1898 | 42 | 1898 | 43 | 27 | 62.7907 | |
| qzeng-custom | INDEL | I6_15 | map_l100_m1_e0 | homalt | 61.0583 | 75.7576 | 51.1364 | 71.4286 | 25 | 8 | 45 | 43 | 0 | 0.0000 | |
| qzeng-custom | INDEL | I6_15 | map_l100_m2_e0 | homalt | 61.4480 | 75.7576 | 51.6854 | 73.5905 | 25 | 8 | 46 | 43 | 0 | 0.0000 | |
| qzeng-custom | INDEL | I6_15 | map_l100_m2_e1 | homalt | 61.4480 | 75.7576 | 51.6854 | 74.0525 | 25 | 8 | 46 | 43 | 0 | 0.0000 | |
| qzeng-custom | SNP | * | map_l125_m0_e0 | homalt | 77.7882 | 64.0644 | 98.9949 | 72.2676 | 4300 | 2412 | 4235 | 43 | 42 | 97.6744 | |
| qzeng-custom | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5290 | 99.4853 | 99.5728 | 52.8503 | 10050 | 52 | 10023 | 43 | 23 | 53.4884 | |
| ndellapenna-hhga | INDEL | * | map_l125_m2_e1 | * | 97.7935 | 97.5281 | 98.0604 | 98.3524 | 2170 | 55 | 2174 | 43 | 15 | 34.8837 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 82.9391 | 77.0624 | 89.7862 | 73.3037 | 383 | 114 | 378 | 43 | 27 | 62.7907 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.7010 | 93.8654 | 97.6098 | 62.3325 | 1729 | 113 | 1756 | 43 | 13 | 30.2326 | |
| mlin-fermikit | INDEL | D1_5 | map_l125_m0_e0 | homalt | 67.8201 | 66.2162 | 69.5035 | 79.0490 | 98 | 50 | 98 | 43 | 39 | 90.6977 | |
| mlin-fermikit | INDEL | D6_15 | map_l100_m1_e0 | * | 74.6205 | 69.3798 | 80.7175 | 81.6461 | 179 | 79 | 180 | 43 | 33 | 76.7442 | |
| mlin-fermikit | INDEL | D6_15 | map_l100_m2_e0 | * | 75.2386 | 70.0758 | 81.2227 | 82.7430 | 185 | 79 | 186 | 43 | 33 | 76.7442 | |
| mlin-fermikit | INDEL | D6_15 | map_siren | het | 83.2384 | 82.1429 | 84.3636 | 79.3233 | 230 | 50 | 232 | 43 | 33 | 76.7442 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 82.7354 | 76.8750 | 89.5631 | 81.5825 | 369 | 111 | 369 | 43 | 43 | 100.0000 | |
| mlin-fermikit | INDEL | I1_5 | map_l100_m0_e0 | * | 62.6026 | 49.1713 | 86.1290 | 76.1722 | 267 | 276 | 267 | 43 | 36 | 83.7209 | |
| mlin-fermikit | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 98.3774 | 99.7197 | 97.0708 | 30.6893 | 1423 | 4 | 1425 | 43 | 41 | 95.3488 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 94.5857 | 90.9615 | 98.5106 | 44.8835 | 2838 | 282 | 2844 | 43 | 39 | 90.6977 | |
| ndellapenna-hhga | SNP | ti | map_l150_m2_e1 | * | 99.0741 | 98.3690 | 99.7895 | 74.1500 | 20385 | 338 | 20385 | 43 | 23 | 53.4884 | |
| anovak-vg | INDEL | I6_15 | map_l100_m2_e0 | * | 53.4759 | 49.1379 | 58.6538 | 81.9130 | 57 | 59 | 61 | 43 | 25 | 58.1395 | |
| anovak-vg | INDEL | I6_15 | segdup | homalt | 59.8909 | 80.8511 | 47.5610 | 87.6506 | 38 | 9 | 39 | 43 | 42 | 97.6744 | |
| anovak-vg | SNP | tv | map_l125_m2_e0 | homalt | 89.0712 | 80.8709 | 99.1223 | 69.1421 | 4866 | 1151 | 4856 | 43 | 32 | 74.4186 | |
| anovak-vg | SNP | tv | map_l125_m2_e1 | homalt | 89.1235 | 80.9516 | 99.1306 | 69.1627 | 4917 | 1157 | 4903 | 43 | 32 | 74.4186 | |
| astatham-gatk | SNP | ti | * | homalt | 99.9764 | 99.9582 | 99.9946 | 15.8604 | 802702 | 336 | 802693 | 43 | 41 | 95.3488 | |
| astatham-gatk | SNP | ti | HG002complexvar | het | 98.7599 | 97.5636 | 99.9860 | 17.3084 | 307097 | 7669 | 307042 | 43 | 17 | 39.5349 | |
| asubramanian-gatk | INDEL | * | map_l150_m0_e0 | * | 90.5945 | 89.6887 | 91.5187 | 98.1956 | 461 | 53 | 464 | 43 | 3 | 6.9767 | |
| asubramanian-gatk | INDEL | D16_PLUS | HG002complexvar | * | 96.5513 | 95.8004 | 97.3142 | 67.2463 | 1574 | 69 | 1558 | 43 | 31 | 72.0930 | |
| asubramanian-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.2719 | 98.8007 | 99.7476 | 56.4979 | 16971 | 206 | 16992 | 43 | 6 | 13.9535 | |
| asubramanian-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.0897 | 98.8283 | 99.3524 | 77.3626 | 6579 | 78 | 6597 | 43 | 9 | 20.9302 | |
| bgallagher-sentieon | INDEL | I6_15 | HG002complexvar | homalt | 98.2186 | 99.9176 | 96.5764 | 55.7279 | 1213 | 1 | 1213 | 43 | 43 | 100.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.0609 | 95.3297 | 98.8561 | 56.5082 | 3715 | 182 | 3716 | 43 | 36 | 83.7209 | |