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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
12351-12400 / 86044 show all | |||||||||||||||
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 63.8406 | 59.0164 | 69.5238 | 78.0335 | 72 | 50 | 73 | 32 | 31 | 96.8750 | |
| ghariani-varprowl | INDEL | I1_5 | map_l100_m1_e0 | * | 93.9359 | 94.3241 | 93.5508 | 86.7120 | 1263 | 76 | 1262 | 87 | 31 | 35.6322 | |
| ghariani-varprowl | INDEL | I6_15 | segdup | het | 83.2383 | 97.5904 | 72.5664 | 93.7844 | 81 | 2 | 82 | 31 | 31 | 100.0000 | |
| ghariani-varprowl | SNP | tv | map_l250_m1_e0 | het | 92.9690 | 98.0414 | 88.3956 | 91.8864 | 1752 | 35 | 1752 | 230 | 31 | 13.4783 | |
| gduggal-snapvard | INDEL | C1_5 | * | homalt | 0.0000 | 0.0000 | 93.2755 | 88.9976 | 0 | 0 | 860 | 62 | 31 | 50.0000 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 84.4875 | 91.0761 | 78.7879 | 71.3873 | 694 | 68 | 702 | 189 | 31 | 16.4021 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 73.8072 | 96.5392 | 59.7403 | 70.7317 | 530 | 19 | 552 | 372 | 31 | 8.3333 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 53.0409 | 42.6966 | 70.0000 | 56.1753 | 76 | 102 | 77 | 33 | 31 | 93.9394 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 73.5213 | 72.9508 | 74.1007 | 51.5679 | 89 | 33 | 103 | 36 | 31 | 86.1111 | |
| gduggal-snapvard | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 76.2490 | 94.7944 | 63.7727 | 85.1927 | 2859 | 157 | 2850 | 1619 | 31 | 1.9148 | |
| gduggal-snapvard | SNP | ti | map_l100_m1_e0 | homalt | 97.9288 | 96.1470 | 99.7778 | 60.0714 | 17268 | 692 | 17067 | 38 | 31 | 81.5789 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 29.7662 | 18.0480 | 84.8708 | 63.2791 | 233 | 1058 | 230 | 41 | 31 | 75.6098 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 55.2595 | 38.9041 | 95.3409 | 37.9408 | 852 | 1338 | 839 | 41 | 31 | 75.6098 | |
| gduggal-snapvard | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.3899 | 98.2619 | 98.5182 | 61.1046 | 6897 | 122 | 6848 | 103 | 31 | 30.0971 | |
| gduggal-snapvard | SNP | tv | map_l250_m2_e0 | * | 84.9127 | 95.5933 | 76.3788 | 91.3348 | 2755 | 127 | 2742 | 848 | 31 | 3.6557 | |
| gduggal-snapvard | SNP | tv | map_l250_m2_e1 | * | 84.9786 | 95.5761 | 76.4966 | 91.4134 | 2787 | 129 | 2773 | 852 | 31 | 3.6385 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | * | 20.9302 | 19.5652 | 22.5000 | 62.6168 | 9 | 37 | 9 | 31 | 31 | 100.0000 | |
| rpoplin-dv42 | SNP | tv | map_l250_m2_e0 | * | 97.9798 | 97.6058 | 98.3566 | 87.5544 | 2813 | 69 | 2813 | 47 | 31 | 65.9574 | |
| rpoplin-dv42 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.8560 | 99.8560 | 99.8559 | 61.0125 | 35368 | 51 | 35352 | 51 | 31 | 60.7843 | |
| rpoplin-dv42 | SNP | * | map_l150_m1_e0 | homalt | 99.3277 | 98.9444 | 99.7139 | 71.2907 | 11154 | 119 | 11154 | 32 | 31 | 96.8750 | |
| rpoplin-dv42 | SNP | * | segdup | * | 99.7488 | 99.7506 | 99.7470 | 89.9398 | 27997 | 70 | 27991 | 71 | 31 | 43.6620 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 97.0477 | 98.7673 | 95.3869 | 67.3469 | 641 | 8 | 641 | 31 | 31 | 100.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.9637 | 97.9911 | 97.9364 | 69.6975 | 1756 | 36 | 1756 | 37 | 31 | 83.7838 | |
| ckim-vqsr | SNP | * | map_siren | * | 85.1088 | 74.3093 | 99.5811 | 71.1680 | 108661 | 37567 | 108641 | 457 | 31 | 6.7834 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5071 | 99.8869 | 99.1302 | 72.8167 | 3533 | 4 | 3533 | 31 | 31 | 100.0000 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.4424 | 99.5121 | 99.3729 | 70.5814 | 45479 | 223 | 45479 | 287 | 31 | 10.8014 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.4424 | 99.5121 | 99.3729 | 70.5814 | 45479 | 223 | 45479 | 287 | 31 | 10.8014 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 72.9624 | 58.1711 | 97.8403 | 43.0063 | 1584 | 1139 | 1495 | 33 | 31 | 93.9394 | |
| egarrison-hhga | INDEL | * | map_l100_m2_e1 | het | 97.4787 | 97.9513 | 97.0105 | 84.5478 | 2295 | 48 | 2304 | 71 | 31 | 43.6620 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 87.8990 | 80.2937 | 97.0958 | 47.6367 | 1039 | 255 | 1237 | 37 | 31 | 83.7838 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 95.0368 | 92.4855 | 97.7328 | 30.1370 | 1600 | 130 | 1595 | 37 | 31 | 83.7838 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 63.1996 | 46.4567 | 98.8107 | 36.5459 | 3304 | 3808 | 2908 | 35 | 31 | 88.5714 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 87.7109 | 81.5789 | 94.8396 | 65.2279 | 682 | 154 | 680 | 37 | 31 | 83.7838 | |
| egarrison-hhga | SNP | * | HG002compoundhet | het | 98.5499 | 97.5455 | 99.5752 | 43.4625 | 13830 | 348 | 13830 | 59 | 31 | 52.5424 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 95.7529 | 94.2568 | 97.2973 | 83.7363 | 2232 | 136 | 2232 | 62 | 31 | 50.0000 | |
| egarrison-hhga | SNP | * | map_l100_m1_e0 | het | 99.3656 | 98.9352 | 99.7999 | 63.8790 | 44876 | 483 | 44877 | 90 | 31 | 34.4444 | |
| egarrison-hhga | SNP | * | map_l100_m2_e0 | het | 99.3648 | 98.9461 | 99.7870 | 65.4283 | 45910 | 489 | 45911 | 98 | 31 | 31.6327 | |
| egarrison-hhga | SNP | * | map_l100_m2_e1 | het | 99.3694 | 98.9552 | 99.7871 | 65.4429 | 46408 | 490 | 46409 | 99 | 31 | 31.3131 | |
| egarrison-hhga | SNP | ti | map_l100_m1_e0 | * | 99.5648 | 99.2719 | 99.8594 | 62.6430 | 47582 | 349 | 47583 | 67 | 31 | 46.2687 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9850 | 98.7098 | 99.2618 | 74.4815 | 14383 | 188 | 14387 | 107 | 31 | 28.9720 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9850 | 98.7098 | 99.2618 | 74.4815 | 14383 | 188 | 14387 | 107 | 31 | 28.9720 | |
| eyeh-varpipe | INDEL | * | map_l125_m1_e0 | homalt | 97.0129 | 97.1311 | 96.8950 | 86.7449 | 711 | 21 | 1061 | 34 | 31 | 91.1765 | |
| eyeh-varpipe | INDEL | * | segdup | het | 96.4604 | 95.6344 | 97.3009 | 93.4137 | 1402 | 64 | 1478 | 41 | 31 | 75.6098 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 94.2166 | 90.2898 | 98.5006 | 65.6575 | 25924 | 2788 | 26146 | 398 | 31 | 7.7889 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 94.2166 | 90.2898 | 98.5006 | 65.6575 | 25924 | 2788 | 26146 | 398 | 31 | 7.7889 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 96.8519 | 94.5071 | 99.3160 | 27.2218 | 6951 | 404 | 6970 | 48 | 31 | 64.5833 | |
| ckim-isaac | SNP | ti | * | het | 98.7325 | 97.5284 | 99.9667 | 15.6908 | 1250214 | 31683 | 1250525 | 417 | 31 | 7.4341 | |
| bgallagher-sentieon | INDEL | D16_PLUS | HG002complexvar | * | 97.3999 | 97.3828 | 97.4170 | 66.7553 | 1600 | 43 | 1584 | 42 | 31 | 73.8095 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.5221 | 95.5960 | 99.5274 | 32.5866 | 6512 | 300 | 6529 | 31 | 31 | 100.0000 | |
| asubramanian-gatk | INDEL | D16_PLUS | * | hetalt | 95.6218 | 93.1712 | 98.2048 | 39.4536 | 1801 | 132 | 2024 | 37 | 31 | 83.7838 | |