PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
39451-39500 / 86044 show all | |||||||||||||||
| asubramanian-gatk | INDEL | * | map_l125_m2_e1 | het | 88.1973 | 83.0256 | 94.0562 | 92.2786 | 1169 | 239 | 1171 | 74 | 7 | 9.4595 | |
| gduggal-snapplat | INDEL | D1_5 | * | het | 85.0942 | 83.0201 | 87.2745 | 66.1285 | 72704 | 14870 | 86462 | 12607 | 2010 | 15.9435 | |
| gduggal-snapplat | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 90.1136 | 83.0190 | 98.5341 | 67.6995 | 16769 | 3430 | 16804 | 250 | 110 | 44.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | map_l125_m1_e0 | * | 89.7959 | 83.0189 | 97.7778 | 90.5263 | 44 | 9 | 44 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | map_l125_m2_e0 | * | 89.7959 | 83.0189 | 97.7778 | 91.7279 | 44 | 9 | 44 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | map_l125_m2_e1 | * | 89.7959 | 83.0189 | 97.7778 | 91.9643 | 44 | 9 | 44 | 1 | 1 | 100.0000 | |
| rpoplin-dv42 | INDEL | I6_15 | map_l125_m1_e0 | * | 88.0000 | 83.0189 | 93.6170 | 89.3905 | 44 | 9 | 44 | 3 | 2 | 66.6667 | |
| rpoplin-dv42 | INDEL | I6_15 | map_l125_m2_e0 | * | 88.0000 | 83.0189 | 93.6170 | 90.5242 | 44 | 9 | 44 | 3 | 2 | 66.6667 | |
| rpoplin-dv42 | INDEL | I6_15 | map_l125_m2_e1 | * | 88.0000 | 83.0189 | 93.6170 | 90.8382 | 44 | 9 | 44 | 3 | 2 | 66.6667 | |
| rpoplin-dv42 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 87.0071 | 83.0189 | 91.3978 | 81.9767 | 88 | 18 | 85 | 8 | 8 | 100.0000 | |
| mlin-fermikit | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 79.4582 | 83.0189 | 76.1905 | 81.2500 | 88 | 18 | 80 | 25 | 25 | 100.0000 | |
| raldana-dualsentieon | INDEL | I6_15 | map_l125_m1_e0 | * | 88.8889 | 83.0189 | 95.6522 | 88.3838 | 44 | 9 | 44 | 2 | 0 | 0.0000 | |
| raldana-dualsentieon | INDEL | I6_15 | map_l125_m2_e0 | * | 88.8889 | 83.0189 | 95.6522 | 89.6861 | 44 | 9 | 44 | 2 | 0 | 0.0000 | |
| raldana-dualsentieon | INDEL | I6_15 | map_l125_m2_e1 | * | 88.8889 | 83.0189 | 95.6522 | 89.9563 | 44 | 9 | 44 | 2 | 0 | 0.0000 | |
| gduggal-snapvard | INDEL | * | map_siren | homalt | 89.9289 | 83.0132 | 98.1015 | 71.6674 | 2204 | 451 | 2377 | 46 | 40 | 86.9565 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 75.3753 | 83.0063 | 69.0293 | 65.5447 | 6980 | 1429 | 5639 | 2530 | 425 | 16.7984 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 87.3110 | 82.9974 | 92.0976 | 77.0179 | 947 | 194 | 944 | 81 | 55 | 67.9012 | |
| egarrison-hhga | INDEL | I16_PLUS | HG002compoundhet | hetalt | 90.3511 | 82.9909 | 99.1438 | 40.2252 | 1737 | 356 | 1737 | 15 | 11 | 73.3333 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 85.4625 | 82.9902 | 88.0866 | 50.9735 | 766 | 157 | 244 | 33 | 29 | 87.8788 | |
| asubramanian-gatk | INDEL | I1_5 | map_siren | het | 89.9163 | 82.9863 | 98.1092 | 85.7556 | 1395 | 286 | 1401 | 27 | 5 | 18.5185 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 83.6346 | 82.9843 | 84.2953 | 47.3907 | 18464 | 3786 | 18534 | 3453 | 3234 | 93.6577 | |
| gduggal-bwaplat | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 90.5878 | 82.9794 | 99.7323 | 63.7829 | 16761 | 3438 | 16763 | 45 | 38 | 84.4444 | |
| gduggal-bwaplat | INDEL | I6_15 | segdup | homalt | 90.6977 | 82.9787 | 100.0000 | 93.1860 | 39 | 8 | 37 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | D1_5 | map_l100_m1_e0 | hetalt | 90.6977 | 82.9787 | 100.0000 | 93.6027 | 39 | 8 | 38 | 0 | 0 | ||
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 85.5631 | 82.9787 | 88.3137 | 74.1798 | 1131 | 232 | 1126 | 149 | 144 | 96.6443 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 90.6977 | 82.9787 | 100.0000 | 65.2174 | 39 | 8 | 40 | 0 | 0 | ||
| anovak-vg | INDEL | D6_15 | map_l150_m2_e1 | het | 79.8362 | 82.9787 | 76.9231 | 92.2619 | 39 | 8 | 40 | 12 | 7 | 58.3333 | |
| ciseli-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | homalt | 45.6140 | 82.9787 | 31.4516 | 52.4904 | 39 | 8 | 39 | 85 | 76 | 89.4118 | |
| gduggal-snapvard | INDEL | D1_5 | HG002compoundhet | het | 70.6222 | 82.9664 | 61.4755 | 58.2800 | 1432 | 294 | 12099 | 7582 | 5798 | 76.4706 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 83.9138 | 82.9573 | 84.8926 | 46.2434 | 18458 | 3792 | 18538 | 3299 | 3068 | 92.9979 | |
| ciseli-custom | SNP | tv | map_l150_m2_e0 | homalt | 85.5692 | 82.9537 | 88.3551 | 74.3676 | 3387 | 696 | 3384 | 446 | 347 | 77.8027 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 87.2012 | 82.9480 | 91.9141 | 36.2721 | 1435 | 295 | 1455 | 128 | 122 | 95.3125 | |
| astatham-gatk | SNP | * | map_l150_m0_e0 | het | 90.3676 | 82.9471 | 99.2462 | 85.7275 | 6586 | 1354 | 6583 | 50 | 12 | 24.0000 | |
| ciseli-custom | SNP | tv | map_l150_m2_e1 | homalt | 85.5896 | 82.9463 | 88.4069 | 74.3629 | 3429 | 705 | 3424 | 449 | 348 | 77.5056 | |
| gduggal-snapplat | SNP | ti | map_l250_m1_e0 | * | 88.1520 | 82.9439 | 94.0579 | 93.4361 | 3798 | 781 | 3799 | 240 | 126 | 52.5000 | |
| qzeng-custom | INDEL | I16_PLUS | * | * | 83.4199 | 82.9387 | 83.9068 | 61.2425 | 5289 | 1088 | 5292 | 1015 | 362 | 35.6650 | |
| asubramanian-gatk | INDEL | * | map_l250_m2_e1 | het | 83.7321 | 82.9384 | 84.5411 | 97.5144 | 175 | 36 | 175 | 32 | 3 | 9.3750 | |
| jpowers-varprowl | INDEL | I6_15 | HG002complexvar | het | 76.9804 | 82.9299 | 71.8274 | 56.3262 | 1953 | 402 | 1981 | 777 | 772 | 99.3565 | |
| ltrigg-rtg2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 90.6667 | 82.9268 | 100.0000 | 88.6861 | 34 | 7 | 31 | 0 | 0 | ||
| qzeng-custom | INDEL | D6_15 | map_l150_m2_e0 | * | 84.5874 | 82.9268 | 86.3158 | 93.7949 | 68 | 14 | 82 | 13 | 6 | 46.1538 | |
| gduggal-bwavard | INDEL | D6_15 | map_l150_m2_e0 | * | 82.8213 | 82.9268 | 82.7160 | 93.4835 | 68 | 14 | 67 | 14 | 10 | 71.4286 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 90.6667 | 82.9268 | 100.0000 | 53.4653 | 272 | 56 | 47 | 0 | 0 | ||
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 45.1741 | 82.9268 | 31.0421 | 68.1047 | 136 | 28 | 140 | 311 | 310 | 99.6785 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 88.3117 | 82.9268 | 94.4444 | 87.1429 | 34 | 7 | 34 | 2 | 1 | 50.0000 | |
| qzeng-custom | INDEL | D6_15 | HG002compoundhet | * | 81.7565 | 82.9255 | 80.6200 | 31.3934 | 7489 | 1542 | 8582 | 2063 | 963 | 46.6796 | |
| qzeng-custom | INDEL | I1_5 | map_siren | homalt | 90.0289 | 82.9208 | 98.4698 | 74.4832 | 1005 | 207 | 1094 | 17 | 4 | 23.5294 | |
| qzeng-custom | INDEL | * | HG002complexvar | hetalt | 90.0705 | 82.9143 | 98.5786 | 66.1860 | 3067 | 632 | 1179 | 17 | 13 | 76.4706 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 79.3428 | 82.9101 | 76.0698 | 72.6664 | 5322 | 1097 | 5404 | 1700 | 930 | 54.7059 | |
| ciseli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 79.3428 | 82.9101 | 76.0698 | 72.6664 | 5322 | 1097 | 5404 | 1700 | 930 | 54.7059 | |
| gduggal-snapplat | SNP | tv | HG002compoundhet | het | 71.6435 | 82.9018 | 63.0774 | 69.0248 | 3874 | 799 | 3919 | 2294 | 156 | 6.8004 | |