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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
71751-71800 / 86044 show all | |||||||||||||||
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.0410 | 89.1557 | 99.4928 | 31.2609 | 1151 | 140 | 1177 | 6 | 5 | 83.3333 | |
| ckim-vqsr | INDEL | D16_PLUS | * | * | 97.9266 | 97.9363 | 97.9170 | 71.5505 | 6644 | 140 | 6628 | 141 | 105 | 74.4681 | |
| ckim-isaac | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.5412 | 91.9336 | 99.4434 | 50.8361 | 1607 | 141 | 1608 | 9 | 7 | 77.7778 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 97.1896 | 94.7427 | 99.7662 | 39.0209 | 2541 | 141 | 2560 | 6 | 6 | 100.0000 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 67.2854 | 50.6993 | 100.0000 | 38.7234 | 145 | 141 | 144 | 0 | 0 | ||
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 40.4624 | 33.1754 | 51.8519 | 75.6757 | 70 | 141 | 70 | 65 | 58 | 89.2308 | |
| jpowers-varprowl | SNP | ti | map_l100_m0_e0 | homalt | 99.0013 | 98.1863 | 99.8300 | 65.3054 | 7633 | 141 | 7633 | 13 | 10 | 76.9231 | |
| jpowers-varprowl | SNP | ti | segdup | * | 98.3696 | 99.2783 | 97.4774 | 91.2225 | 19396 | 141 | 19398 | 502 | 38 | 7.5697 | |
| jpowers-varprowl | SNP | tv | map_l150_m0_e0 | het | 93.9990 | 95.0405 | 92.9800 | 87.0071 | 2702 | 141 | 2702 | 204 | 53 | 25.9804 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 98.4486 | 97.4071 | 99.5127 | 25.8925 | 5297 | 141 | 5309 | 26 | 25 | 96.1538 | |
| jpowers-varprowl | INDEL | D1_5 | map_l100_m1_e0 | * | 93.6112 | 92.3701 | 94.8860 | 83.6796 | 1707 | 141 | 1707 | 92 | 63 | 68.4783 | |
| ciseli-custom | SNP | tv | segdup | het | 93.4710 | 97.3331 | 89.9038 | 92.8401 | 5146 | 141 | 5138 | 577 | 16 | 2.7730 | |
| gduggal-bwafb | INDEL | * | map_l100_m2_e0 | het | 95.9110 | 93.8882 | 98.0228 | 83.5180 | 2166 | 141 | 2231 | 45 | 7 | 15.5556 | |
| mlin-fermikit | INDEL | * | map_l250_m2_e1 | het | 48.4429 | 33.1754 | 89.7436 | 93.5537 | 70 | 141 | 70 | 8 | 1 | 12.5000 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 80.6298 | 89.3985 | 73.4276 | 74.6915 | 1189 | 141 | 1039 | 376 | 353 | 93.8830 | |
| astatham-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.3358 | 98.7667 | 99.9115 | 42.6185 | 11292 | 141 | 11289 | 10 | 2 | 20.0000 | |
| astatham-gatk | SNP | * | map_l100_m0_e0 | homalt | 99.3208 | 98.7866 | 99.8608 | 60.2139 | 11479 | 141 | 11479 | 16 | 12 | 75.0000 | |
| asubramanian-gatk | INDEL | D16_PLUS | HG002compoundhet | * | 94.4206 | 93.9769 | 94.8685 | 35.6370 | 2200 | 141 | 2200 | 119 | 109 | 91.5966 | |
| asubramanian-gatk | INDEL | I1_5 | map_l125_m2_e1 | * | 90.3357 | 83.7931 | 97.9866 | 90.5301 | 729 | 141 | 730 | 15 | 1 | 6.6667 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 95.2682 | 92.0384 | 98.7330 | 37.3051 | 1630 | 141 | 2104 | 27 | 26 | 96.2963 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 96.3287 | 96.4131 | 96.2444 | 58.5642 | 3790 | 141 | 3844 | 150 | 63 | 42.0000 | |
| anovak-vg | SNP | * | segdup | homalt | 98.7938 | 98.6875 | 98.9004 | 87.8317 | 10602 | 141 | 10523 | 117 | 108 | 92.3077 | |
| anovak-vg | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 90.5371 | 93.0336 | 88.1711 | 73.4829 | 1883 | 141 | 1938 | 260 | 97 | 37.3077 | |
| anovak-vg | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 96.4762 | 96.4847 | 96.4677 | 49.2144 | 3870 | 141 | 3960 | 145 | 74 | 51.0345 | |
| astatham-gatk | INDEL | * | * | homalt | 99.5755 | 99.8874 | 99.2657 | 58.8575 | 125031 | 141 | 125041 | 925 | 908 | 98.1622 | |
| hfeng-pmm1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.1484 | 94.6692 | 99.7610 | 81.1745 | 2504 | 141 | 2504 | 6 | 4 | 66.6667 | |
| jlack-gatk | SNP | ti | map_l150_m2_e0 | het | 94.5791 | 98.9054 | 90.6154 | 86.2755 | 12740 | 141 | 12736 | 1319 | 117 | 8.8704 | |
| jlack-gatk | SNP | ti | map_l150_m2_e1 | het | 94.5873 | 98.9166 | 90.6210 | 86.3363 | 12874 | 141 | 12870 | 1332 | 118 | 8.8589 | |
| jlack-gatk | SNP | tv | map_l100_m0_e0 | * | 94.2911 | 98.7279 | 90.2359 | 79.7630 | 10943 | 141 | 10942 | 1184 | 68 | 5.7432 | |
| raldana-dualsentieon | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9397 | 98.7667 | 99.1133 | 38.6843 | 11292 | 141 | 11289 | 101 | 1 | 0.9901 | |
| rpoplin-dv42 | INDEL | * | map_siren | * | 98.4035 | 98.0972 | 98.7117 | 97.1910 | 7269 | 141 | 7279 | 95 | 49 | 51.5789 | |
| rpoplin-dv42 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 91.6249 | 85.0636 | 99.2832 | 28.0928 | 803 | 141 | 831 | 6 | 6 | 100.0000 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 88.9064 | 83.4507 | 95.1253 | 86.7650 | 711 | 141 | 683 | 35 | 18 | 51.4286 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 38.7893 | 24.1935 | 97.7778 | 41.5584 | 45 | 141 | 44 | 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 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 60.3322 | 92.2485 | 44.8239 | 74.0840 | 1678 | 141 | 1693 | 2084 | 2043 | 98.0326 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 60.3322 | 92.2485 | 44.8239 | 74.0840 | 1678 | 141 | 1693 | 2084 | 2043 | 98.0326 | |
| ghariani-varprowl | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 49.8073 | 85.3306 | 35.1672 | 63.7131 | 826 | 142 | 831 | 1532 | 1487 | 97.0627 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 13.3942 | 7.1895 | 97.7778 | 42.3077 | 11 | 142 | 44 | 1 | 1 | 100.0000 | |
| gduggal-snapvard | SNP | * | map_l250_m0_e0 | * | 79.3745 | 93.3489 | 69.0393 | 94.3087 | 1993 | 142 | 1969 | 883 | 24 | 2.7180 | |
| ghariani-varprowl | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 96.5798 | 99.2191 | 94.0773 | 54.5022 | 18041 | 142 | 18092 | 1139 | 144 | 12.6427 | |
| gduggal-snapfb | SNP | * | map_l250_m0_e0 | * | 93.7882 | 93.3489 | 94.2317 | 93.9033 | 1993 | 142 | 1993 | 122 | 43 | 35.2459 | |
| gduggal-snapfb | SNP | * | segdup | * | 98.9601 | 99.4941 | 98.4319 | 91.5712 | 27925 | 142 | 27933 | 445 | 34 | 7.6405 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 22.9391 | 31.0680 | 18.1818 | 56.7921 | 64 | 142 | 48 | 216 | 4 | 1.8519 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | * | hetalt | 95.7476 | 92.6539 | 99.0550 | 39.6309 | 1791 | 142 | 1782 | 17 | 17 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.7426 | 92.6463 | 99.0529 | 39.5216 | 1789 | 142 | 1778 | 17 | 17 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.7426 | 92.6463 | 99.0529 | 39.5216 | 1789 | 142 | 1778 | 17 | 17 | 100.0000 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 85.3371 | 87.1377 | 83.6094 | 85.7161 | 962 | 142 | 959 | 188 | 129 | 68.6170 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 0.0000 | 82.0933 | 0.0000 | 0.0000 | 651 | 142 | 0 | 0 | 0 | ||
| qzeng-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 76.0681 | 70.4167 | 82.7057 | 61.6372 | 338 | 142 | 1186 | 248 | 176 | 70.9677 | |