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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
1301-1350 / 86044 show all | |||||||||||||||
| ciseli-custom | SNP | * | map_l125_m0_e0 | * | 77.7410 | 73.0049 | 83.1343 | 80.5630 | 14152 | 5233 | 14132 | 2867 | 775 | 27.0317 | |
| ciseli-custom | INDEL | D1_5 | HG002compoundhet | het | 30.2760 | 33.1981 | 27.8267 | 77.5472 | 573 | 1153 | 1105 | 2866 | 1255 | 43.7893 | |
| gduggal-bwaplat | SNP | tv | * | het | 98.5255 | 97.5640 | 99.5062 | 36.2003 | 577282 | 14414 | 577577 | 2866 | 351 | 12.2470 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 33.6989 | 27.4371 | 43.6639 | 50.1227 | 1669 | 4414 | 2219 | 2863 | 2250 | 78.5889 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 58.5321 | 47.8735 | 75.2959 | 43.8204 | 2544 | 2770 | 8714 | 2859 | 2841 | 99.3704 | |
| ckim-isaac | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 94.4269 | 92.1672 | 96.8002 | 61.2699 | 87051 | 7398 | 86368 | 2855 | 2059 | 72.1191 | |
| cchapple-custom | SNP | * | map_siren | * | 98.2653 | 98.4743 | 98.0572 | 58.9696 | 143997 | 2231 | 143999 | 2853 | 550 | 19.2780 | |
| anovak-vg | SNP | tv | map_l100_m0_e0 | het | 78.7491 | 90.6120 | 69.6328 | 77.9564 | 6544 | 678 | 6542 | 2853 | 767 | 26.8840 | |
| qzeng-custom | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 79.5976 | 80.1449 | 79.0576 | 60.6684 | 8073 | 2000 | 10755 | 2849 | 1405 | 49.3155 | |
| gduggal-snapplat | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 27.4935 | 24.7277 | 30.9558 | 84.2395 | 999 | 3041 | 1276 | 2846 | 368 | 12.9304 | |
| cchapple-custom | SNP | * | map_siren | het | 97.7546 | 98.5944 | 96.9290 | 63.2688 | 89712 | 1279 | 89826 | 2846 | 543 | 19.0794 | |
| gduggal-snapplat | SNP | * | map_siren | * | 96.8913 | 95.7977 | 98.0103 | 67.7918 | 140083 | 6145 | 140139 | 2845 | 1340 | 47.1002 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 49.1489 | 40.2731 | 63.0429 | 36.1826 | 2389 | 3543 | 4848 | 2842 | 2348 | 82.6179 | |
| rpoplin-dv42 | INDEL | * | * | * | 98.9802 | 98.7882 | 99.1728 | 78.6199 | 340367 | 4175 | 340370 | 2839 | 2640 | 92.9905 | |
| anovak-vg | SNP | * | map_l250_m2_e1 | * | 75.2143 | 81.7954 | 69.6133 | 91.5868 | 6533 | 1454 | 6481 | 2829 | 654 | 23.1177 | |
| ciseli-custom | SNP | * | map_l100_m0_e0 | het | 77.1628 | 71.2049 | 84.2088 | 78.9054 | 15099 | 6106 | 15086 | 2829 | 99 | 3.4995 | |
| gduggal-snapvard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 82.0117 | 91.2515 | 74.4710 | 86.1394 | 8334 | 799 | 8235 | 2823 | 102 | 3.6132 | |
| gduggal-snapvard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 82.0117 | 91.2515 | 74.4710 | 86.1394 | 8334 | 799 | 8235 | 2823 | 102 | 3.6132 | |
| gduggal-snapfb | SNP | tv | * | homalt | 99.5195 | 99.7842 | 99.2562 | 25.9790 | 376309 | 814 | 376328 | 2820 | 182 | 6.4539 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 83.5727 | 82.8140 | 84.3455 | 36.4989 | 15121 | 3138 | 15194 | 2820 | 2630 | 93.2624 | |
| ciseli-custom | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 91.5338 | 92.8273 | 90.2759 | 58.4295 | 26233 | 2027 | 26180 | 2820 | 1567 | 55.5674 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 32.5229 | 33.1367 | 31.9314 | 80.3989 | 1292 | 2607 | 1321 | 2816 | 99 | 3.5156 | |
| anovak-vg | SNP | * | map_l250_m2_e1 | het | 71.9604 | 86.4932 | 61.6087 | 92.1600 | 4553 | 711 | 4519 | 2816 | 645 | 22.9048 | |
| qzeng-custom | INDEL | D16_PLUS | * | * | 79.4045 | 91.9517 | 69.8705 | 62.5471 | 6238 | 546 | 6528 | 2815 | 413 | 14.6714 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 70.2794 | 91.7657 | 56.9459 | 43.6183 | 1081 | 97 | 3718 | 2811 | 2776 | 98.7549 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 63.5703 | 52.8321 | 79.7871 | 32.1688 | 3134 | 2798 | 11092 | 2810 | 2788 | 99.2171 | |
| gduggal-snapplat | SNP | * | map_siren | het | 96.5899 | 96.2777 | 96.9043 | 72.4626 | 87604 | 3387 | 87710 | 2802 | 1309 | 46.7166 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 88.0966 | 87.6813 | 88.5158 | 38.7217 | 21517 | 3023 | 21589 | 2801 | 2559 | 91.3602 | |
| anovak-vg | SNP | * | map_l250_m2_e0 | * | 75.1311 | 81.7121 | 69.5312 | 91.5463 | 6443 | 1442 | 6392 | 2801 | 650 | 23.2060 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 77.4749 | 88.1419 | 69.1110 | 56.7739 | 5887 | 792 | 6258 | 2797 | 1501 | 53.6646 | |
| ciseli-custom | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 51.2986 | 77.9991 | 38.2164 | 61.6156 | 1723 | 486 | 1727 | 2792 | 2527 | 90.5086 | |
| anovak-vg | SNP | * | map_l250_m2_e0 | het | 71.8617 | 86.4074 | 61.5077 | 92.1188 | 4488 | 706 | 4455 | 2788 | 641 | 22.9914 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 16.5768 | 23.8066 | 12.7153 | 80.3047 | 384 | 1229 | 406 | 2787 | 32 | 1.1482 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 67.1072 | 91.8336 | 52.8714 | 33.4573 | 596 | 53 | 3121 | 2782 | 2751 | 98.8857 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 95.2637 | 99.3096 | 91.5345 | 77.9592 | 30928 | 215 | 29962 | 2771 | 142 | 5.1245 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 95.2637 | 99.3096 | 91.5345 | 77.9592 | 30928 | 215 | 29962 | 2771 | 142 | 5.1245 | |
| gduggal-bwafb | INDEL | * | * | homalt | 98.0353 | 98.2688 | 97.8029 | 56.6087 | 123005 | 2167 | 122991 | 2763 | 2706 | 97.9370 | |
| gduggal-snapplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 59.2248 | 49.9739 | 72.6787 | 68.3719 | 5739 | 5745 | 7342 | 2760 | 1993 | 72.2101 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 85.8009 | 91.8776 | 80.4781 | 48.4090 | 11504 | 1017 | 11378 | 2760 | 2725 | 98.7319 | |
| jmaeng-gatk | INDEL | * | * | * | 99.1098 | 99.0216 | 99.1981 | 60.9184 | 341171 | 3371 | 341038 | 2757 | 1621 | 58.7958 | |
| cchapple-custom | SNP | ti | * | * | 99.8773 | 99.8866 | 99.8679 | 19.3368 | 2083147 | 2364 | 2081936 | 2754 | 477 | 17.3203 | |
| anovak-vg | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.1202 | 97.0035 | 95.2529 | 60.1354 | 53964 | 1667 | 55240 | 2753 | 1338 | 48.6015 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 84.1727 | 99.6274 | 72.8688 | 27.5370 | 7220 | 27 | 7394 | 2753 | 2746 | 99.7457 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 47.4578 | 43.6627 | 51.9755 | 51.4637 | 2656 | 3427 | 2973 | 2747 | 2524 | 91.8821 | |
| mlin-fermikit | INDEL | * | HG002complexvar | * | 95.4305 | 94.5346 | 96.3436 | 54.3245 | 72733 | 4205 | 72356 | 2746 | 2618 | 95.3387 | |
| jlack-gatk | SNP | ti | map_siren | * | 98.3403 | 99.3782 | 97.3238 | 62.0115 | 99731 | 624 | 99716 | 2742 | 240 | 8.7527 | |
| gduggal-snapfb | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 51.9003 | 97.6253 | 35.3454 | 76.8757 | 1480 | 36 | 1499 | 2742 | 30 | 1.0941 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 89.1102 | 86.0761 | 92.3660 | 60.6253 | 26236 | 4244 | 33152 | 2740 | 2400 | 87.5912 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 89.1102 | 86.0761 | 92.3660 | 60.6253 | 26236 | 4244 | 33152 | 2740 | 2400 | 87.5912 | |
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 87.7327 | 97.7687 | 79.5653 | 85.1430 | 10560 | 241 | 10653 | 2736 | 243 | 8.8816 | |