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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
66951-67000 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.5454 | 94.9673 | 98.1769 | 85.0222 | 1453 | 77 | 1454 | 27 | 18 | 66.6667 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.5454 | 94.9673 | 98.1769 | 85.0222 | 1453 | 77 | 1454 | 27 | 18 | 66.6667 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.9112 | 96.6495 | 99.2063 | 75.8157 | 375 | 13 | 375 | 3 | 2 | 66.6667 | |
| ckim-vqsr | INDEL | I1_5 | map_l100_m0_e0 | homalt | 99.2840 | 100.0000 | 98.5782 | 81.2278 | 208 | 0 | 208 | 3 | 2 | 66.6667 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.5441 | 97.3505 | 99.7673 | 61.8300 | 1286 | 35 | 1286 | 3 | 2 | 66.6667 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 97.3822 | 96.3731 | 98.4127 | 91.0490 | 372 | 14 | 372 | 6 | 4 | 66.6667 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 97.0803 | 96.3768 | 97.7941 | 91.0703 | 266 | 10 | 266 | 6 | 4 | 66.6667 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.6562 | 99.3685 | 99.9455 | 58.6114 | 11014 | 70 | 11010 | 6 | 4 | 66.6667 | |
| ckim-vqsr | SNP | * | map_l125_m1_e0 | homalt | 45.7370 | 29.6539 | 99.9402 | 85.9137 | 5013 | 11892 | 5013 | 3 | 2 | 66.6667 | |
| ckim-vqsr | SNP | * | map_l125_m2_e0 | homalt | 47.0112 | 30.7338 | 99.9439 | 86.8214 | 5340 | 12035 | 5340 | 3 | 2 | 66.6667 | |
| ckim-vqsr | SNP | * | map_l125_m2_e1 | homalt | 47.2295 | 30.9206 | 99.9447 | 86.7543 | 5421 | 12111 | 5421 | 3 | 2 | 66.6667 | |
| ckim-vqsr | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.4469 | 98.9759 | 99.9224 | 33.5509 | 3866 | 40 | 3865 | 3 | 2 | 66.6667 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 80.7339 | 69.2913 | 96.7033 | 44.5122 | 88 | 39 | 88 | 3 | 2 | 66.6667 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 72.7273 | 100.0000 | 57.1429 | 99.9868 | 1 | 0 | 4 | 3 | 2 | 66.6667 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_gt10 | hetalt | 72.7273 | 100.0000 | 57.1429 | 99.7676 | 1 | 0 | 4 | 3 | 2 | 66.6667 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 91.8919 | 86.2944 | 98.2659 | 34.2205 | 170 | 27 | 170 | 3 | 2 | 66.6667 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 86.6039 | 84.2520 | 89.0909 | 56.0000 | 107 | 20 | 98 | 12 | 8 | 66.6667 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 84.5899 | 76.6667 | 94.3396 | 70.0565 | 46 | 14 | 50 | 3 | 2 | 66.6667 | |
| ckim-isaac | INDEL | I1_5 | map_siren | hetalt | 85.4934 | 76.7857 | 96.4286 | 82.2410 | 86 | 26 | 81 | 3 | 2 | 66.6667 | |
| ckim-isaac | INDEL | I1_5 | segdup | * | 97.2169 | 95.6563 | 98.8293 | 93.2182 | 1013 | 46 | 1013 | 12 | 8 | 66.6667 | |
| ckim-isaac | INDEL | I6_15 | map_siren | * | 63.4176 | 46.8852 | 97.9592 | 84.2105 | 143 | 162 | 144 | 3 | 2 | 66.6667 | |
| ckim-isaac | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.1734 | 94.6284 | 99.8591 | 48.1340 | 19114 | 1085 | 19138 | 27 | 18 | 66.6667 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 84.6065 | 77.2727 | 93.4783 | 86.4507 | 85 | 25 | 86 | 6 | 4 | 66.6667 | |
| mlin-fermikit | SNP | tv | lowcmp_SimpleRepeat_diTR_51to200 | * | 57.1429 | 53.8462 | 60.8696 | 96.6667 | 14 | 12 | 14 | 9 | 6 | 66.6667 | |
| mlin-fermikit | SNP | tv | tech_badpromoters | homalt | 95.0000 | 97.4359 | 92.6829 | 49.3827 | 38 | 1 | 38 | 3 | 2 | 66.6667 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 91.9908 | 86.2661 | 98.5294 | 74.4040 | 201 | 32 | 201 | 3 | 2 | 66.6667 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 63.4096 | 46.8051 | 98.2726 | 36.6180 | 586 | 666 | 512 | 9 | 6 | 66.6667 | |
| ndellapenna-hhga | INDEL | * | map_l100_m1_e0 | homalt | 98.4879 | 98.2070 | 98.7705 | 81.8398 | 1205 | 22 | 1205 | 15 | 10 | 66.6667 | |
| ndellapenna-hhga | INDEL | * | map_l100_m2_e0 | homalt | 98.5288 | 98.2554 | 98.8038 | 83.0311 | 1239 | 22 | 1239 | 15 | 10 | 66.6667 | |
| ndellapenna-hhga | INDEL | * | map_l125_m0_e0 | homalt | 98.2456 | 98.5915 | 97.9021 | 86.6480 | 280 | 4 | 280 | 6 | 4 | 66.6667 | |
| ndellapenna-hhga | INDEL | * | map_l150_m1_e0 | homalt | 98.5915 | 98.4848 | 98.6985 | 87.6408 | 455 | 7 | 455 | 6 | 4 | 66.6667 | |
| ndellapenna-hhga | INDEL | * | map_l150_m2_e0 | homalt | 98.6472 | 98.5447 | 98.7500 | 88.7981 | 474 | 7 | 474 | 6 | 4 | 66.6667 | |
| ndellapenna-hhga | INDEL | D16_PLUS | HG002complexvar | hetalt | 58.9170 | 42.1053 | 98.0769 | 57.6087 | 104 | 143 | 153 | 3 | 2 | 66.6667 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 61.4859 | 44.5131 | 99.3789 | 49.1043 | 576 | 718 | 480 | 3 | 2 | 66.6667 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 56.8714 | 40.0911 | 97.8102 | 43.3884 | 176 | 263 | 134 | 3 | 2 | 66.6667 | |
| ndellapenna-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.3763 | 99.3763 | 99.3763 | 54.9625 | 478 | 3 | 478 | 3 | 2 | 66.6667 | |
| ndellapenna-hhga | SNP | tv | map_l125_m0_e0 | homalt | 99.5256 | 99.1896 | 99.8640 | 68.2316 | 2203 | 18 | 2203 | 3 | 2 | 66.6667 | |
| qzeng-custom | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 79.1080 | 66.2395 | 98.1818 | 59.6577 | 2533 | 1291 | 162 | 3 | 2 | 66.6667 | |
| qzeng-custom | INDEL | * | tech_badpromoters | * | 96.0263 | 96.0526 | 96.0000 | 50.9804 | 73 | 3 | 72 | 3 | 2 | 66.6667 | |
| qzeng-custom | INDEL | C1_5 | * | hetalt | 72.7273 | 100.0000 | 57.1429 | 96.7890 | 1 | 0 | 8 | 6 | 4 | 66.6667 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | * | 86.7711 | 82.6667 | 91.3043 | 65.6716 | 62 | 13 | 63 | 6 | 4 | 66.6667 | |
| qzeng-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | het | 82.5611 | 76.9231 | 89.0909 | 67.2619 | 10 | 3 | 49 | 6 | 4 | 66.6667 | |
| qzeng-custom | INDEL | D1_5 | segdup | homalt | 99.3034 | 99.4429 | 99.1643 | 93.1723 | 357 | 2 | 356 | 3 | 2 | 66.6667 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l100_m1_e0 | hetalt | 76.4488 | 65.9574 | 90.9091 | 92.1053 | 31 | 16 | 30 | 3 | 2 | 66.6667 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l100_m2_e0 | hetalt | 75.5177 | 64.5833 | 90.9091 | 92.6829 | 31 | 17 | 30 | 3 | 2 | 66.6667 | |
| ndellapenna-hhga | INDEL | D1_5 | map_l100_m2_e1 | hetalt | 77.1930 | 66.6667 | 91.6667 | 92.2414 | 34 | 17 | 33 | 3 | 2 | 66.6667 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 66.9692 | 50.8453 | 98.0681 | 41.1478 | 1203 | 1163 | 1066 | 21 | 14 | 66.6667 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 60.5363 | 43.5780 | 99.1018 | 34.3811 | 380 | 492 | 331 | 3 | 2 | 66.6667 | |
| ndellapenna-hhga | INDEL | D6_15 | map_l150_m1_e0 | * | 95.2545 | 94.5205 | 96.0000 | 91.2178 | 69 | 4 | 72 | 3 | 2 | 66.6667 | |
| ndellapenna-hhga | INDEL | D6_15 | map_l150_m2_e0 | * | 95.1278 | 93.9024 | 96.3855 | 91.2262 | 77 | 5 | 80 | 3 | 2 | 66.6667 | |