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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
73801-73850 / 86044 show all | |||||||||||||||
| dgrover-gatk | INDEL | * | map_siren | * | 98.9418 | 98.9474 | 98.9362 | 83.4662 | 7332 | 78 | 7347 | 79 | 18 | 22.7848 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 93.5937 | 99.5017 | 88.3481 | 52.5210 | 599 | 3 | 599 | 79 | 78 | 98.7342 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 92.9921 | 92.3939 | 93.5981 | 64.4892 | 1154 | 95 | 1155 | 79 | 58 | 73.4177 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 92.9921 | 92.3939 | 93.5981 | 64.4892 | 1154 | 95 | 1155 | 79 | 58 | 73.4177 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.2567 | 96.6498 | 97.8712 | 70.9851 | 3635 | 126 | 3632 | 79 | 58 | 73.4177 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 82.8877 | 86.3510 | 79.6915 | 44.5869 | 310 | 49 | 310 | 79 | 52 | 65.8228 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.1980 | 95.1981 | 99.2838 | 34.4662 | 10884 | 549 | 10951 | 79 | 11 | 13.9241 | |
| ckim-isaac | SNP | * | map_l100_m2_e0 | het | 81.8136 | 69.3420 | 99.7551 | 67.9608 | 32174 | 14225 | 32181 | 79 | 12 | 15.1899 | |
| ckim-isaac | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 92.5831 | 88.2783 | 97.3293 | 62.2126 | 2779 | 369 | 2879 | 79 | 3 | 3.7975 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 97.2924 | 99.3785 | 95.2920 | 69.4798 | 1599 | 10 | 1599 | 79 | 4 | 5.0633 | |
| gduggal-snapfb | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 2.4691 | 100.0000 | 1.2500 | 60.9756 | 1 | 0 | 1 | 79 | 1 | 1.2658 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 92.7176 | 99.4286 | 86.8552 | 76.5326 | 522 | 3 | 522 | 79 | 2 | 2.5317 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 65.1163 | 73.2026 | 58.6387 | 74.4652 | 112 | 41 | 112 | 79 | 62 | 78.4810 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 88.5630 | 82.2103 | 95.9796 | 32.1478 | 5661 | 1225 | 1886 | 79 | 51 | 64.5570 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 83.0586 | 77.6471 | 89.2809 | 34.5471 | 660 | 190 | 658 | 79 | 79 | 100.0000 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | * | 32.0725 | 30.6667 | 33.6134 | 68.6842 | 23 | 52 | 40 | 79 | 44 | 55.6962 | |
| gduggal-snapplat | INDEL | D1_5 | map_l150_m2_e1 | * | 83.7200 | 78.4062 | 89.8065 | 94.3591 | 610 | 168 | 696 | 79 | 18 | 22.7848 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 73.7755 | 59.7109 | 96.5075 | 47.3586 | 2189 | 1477 | 2183 | 79 | 55 | 69.6203 | |
| ghariani-varprowl | INDEL | D1_5 | map_l125_m0_e0 | * | 90.8918 | 96.5726 | 85.8423 | 90.8419 | 479 | 17 | 479 | 79 | 10 | 12.6582 | |
| gduggal-snapvard | INDEL | D6_15 | map_l100_m2_e0 | het | 76.5318 | 83.2061 | 70.8487 | 83.4554 | 109 | 22 | 192 | 79 | 55 | 69.6203 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 74.0214 | 58.9765 | 99.3707 | 59.0788 | 2086 | 1451 | 12474 | 79 | 71 | 89.8734 | |
| gduggal-snapvard | INDEL | D6_15 | map_l100_m1_e0 | * | 66.5172 | 61.2403 | 72.7891 | 82.3635 | 158 | 100 | 214 | 80 | 56 | 70.0000 | |
| gduggal-snapvard | INDEL | D6_15 | map_l100_m2_e1 | het | 75.7065 | 81.4815 | 70.6960 | 83.7015 | 110 | 25 | 193 | 80 | 56 | 70.0000 | |
| gduggal-snapvard | INDEL | * | func_cds | het | 80.5822 | 87.3832 | 74.7634 | 51.0046 | 187 | 27 | 237 | 80 | 64 | 80.0000 | |
| gduggal-snapvard | INDEL | C1_5 | map_l100_m1_e0 | het | 0.0000 | 0.0000 | 41.1765 | 95.4085 | 0 | 0 | 56 | 80 | 9 | 11.2500 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 69.2765 | 58.7912 | 84.3137 | 82.8571 | 321 | 225 | 430 | 80 | 10 | 12.5000 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 81.7352 | 100.0000 | 69.1120 | 78.6831 | 155 | 0 | 179 | 80 | 5 | 6.2500 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 73.1635 | 81.4815 | 66.3866 | 60.7261 | 88 | 20 | 158 | 80 | 21 | 26.2500 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.0658 | 96.3042 | 97.8396 | 70.2140 | 3622 | 139 | 3623 | 80 | 65 | 81.2500 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.0658 | 96.3042 | 97.8396 | 70.2140 | 3622 | 139 | 3623 | 80 | 65 | 81.2500 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.4344 | 96.9479 | 97.9258 | 61.8911 | 3780 | 119 | 3777 | 80 | 36 | 45.0000 | |
| ndellapenna-hhga | SNP | * | map_l100_m0_e0 | * | 99.0308 | 98.3192 | 99.7529 | 65.5554 | 32289 | 552 | 32290 | 80 | 41 | 51.2500 | |
| ndellapenna-hhga | SNP | * | map_l150_m2_e1 | * | 99.0401 | 98.3421 | 99.7481 | 73.9108 | 31676 | 534 | 31676 | 80 | 40 | 50.0000 | |
| ndellapenna-hhga | SNP | tv | HG002compoundhet | homalt | 98.4034 | 99.1440 | 97.6737 | 43.8897 | 3359 | 29 | 3359 | 80 | 78 | 97.5000 | |
| qzeng-custom | INDEL | * | map_l150_m2_e0 | * | 81.1578 | 71.3778 | 94.0432 | 94.0095 | 1005 | 403 | 1263 | 80 | 39 | 48.7500 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 85.0366 | 86.0656 | 84.0319 | 62.7232 | 420 | 68 | 421 | 80 | 56 | 70.0000 | |
| mlin-fermikit | INDEL | D1_5 | map_l100_m0_e0 | homalt | 70.9924 | 72.0930 | 69.9248 | 75.4613 | 186 | 72 | 186 | 80 | 74 | 92.5000 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 92.3787 | 95.5903 | 89.3758 | 38.2787 | 672 | 31 | 673 | 80 | 79 | 98.7500 | |
| mlin-fermikit | INDEL | I1_5 | map_l100_m2_e1 | * | 72.9543 | 60.7168 | 91.3700 | 78.5863 | 847 | 548 | 847 | 80 | 69 | 86.2500 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 87.0329 | 82.8169 | 91.7012 | 56.1220 | 882 | 183 | 884 | 80 | 65 | 81.2500 | |
| jpowers-varprowl | INDEL | I1_5 | segdup | * | 91.1537 | 90.0850 | 92.2481 | 94.2204 | 954 | 105 | 952 | 80 | 67 | 83.7500 | |
| ltrigg-rtg1 | INDEL | * | HG002complexvar | hetalt | 94.3098 | 90.8354 | 98.0606 | 74.9985 | 3360 | 339 | 4045 | 80 | 79 | 98.7500 | |
| jpowers-varprowl | INDEL | * | map_l150_m2_e1 | het | 92.1590 | 92.8571 | 91.4712 | 91.9353 | 858 | 66 | 858 | 80 | 51 | 63.7500 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 81.5062 | 79.9189 | 83.1579 | 59.0870 | 394 | 99 | 395 | 80 | 78 | 97.5000 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 84.1931 | 94.0741 | 76.1905 | 60.9756 | 254 | 16 | 256 | 80 | 78 | 97.5000 | |
| jpowers-varprowl | INDEL | D1_5 | segdup | * | 91.6633 | 90.7525 | 92.5926 | 94.5780 | 1001 | 102 | 1000 | 80 | 65 | 81.2500 | |
| ltrigg-rtg1 | SNP | * | HG002complexvar | homalt | 99.9052 | 99.8382 | 99.9722 | 19.7176 | 288107 | 467 | 288052 | 80 | 73 | 91.2500 | |
| jmaeng-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.7157 | 99.7174 | 99.7139 | 56.2929 | 27880 | 79 | 27879 | 80 | 10 | 12.5000 | |
| raldana-dualsentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.8505 | 98.2637 | 99.4444 | 73.4266 | 14318 | 253 | 14318 | 80 | 15 | 18.7500 | |
| raldana-dualsentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.8505 | 98.2637 | 99.4444 | 73.4266 | 14318 | 253 | 14318 | 80 | 15 | 18.7500 | |