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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
43851-43900 / 86044 show all | |||||||||||||||
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 46.9083 | 32.3849 | 85.0498 | 32.2072 | 387 | 808 | 256 | 45 | 39 | 86.6667 | |
| jlack-gatk | SNP | * | map_l250_m2_e0 | het | 91.0733 | 98.0169 | 85.0484 | 94.0579 | 5091 | 103 | 5091 | 895 | 58 | 6.4805 | |
| gduggal-snapvard | INDEL | I1_5 | map_l150_m1_e0 | * | 89.6858 | 94.8617 | 85.0455 | 90.4043 | 480 | 26 | 654 | 115 | 40 | 34.7826 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 77.1877 | 70.6598 | 85.0445 | 46.2575 | 6683 | 2775 | 6784 | 1193 | 1020 | 85.4987 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 69.4882 | 58.7467 | 85.0365 | 91.8258 | 225 | 158 | 233 | 41 | 17 | 41.4634 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 80.6871 | 76.7630 | 85.0340 | 31.9444 | 1328 | 402 | 1375 | 242 | 240 | 99.1736 | |
| mlin-fermikit | INDEL | * | map_l150_m2_e1 | * | 65.1571 | 52.8145 | 85.0279 | 85.1378 | 760 | 679 | 761 | 134 | 106 | 79.1045 | |
| mlin-fermikit | SNP | tv | map_l125_m1_e0 | * | 61.8003 | 48.5452 | 85.0126 | 58.2565 | 7775 | 8241 | 7771 | 1370 | 1205 | 87.9562 | |
| jlack-gatk | INDEL | D1_5 | map_l100_m0_e0 | het | 91.3204 | 98.6464 | 85.0073 | 89.4535 | 583 | 8 | 584 | 103 | 5 | 4.8544 | |
| gduggal-snapvard | INDEL | I1_5 | map_l150_m2_e0 | * | 89.7214 | 94.9904 | 85.0062 | 90.8896 | 493 | 26 | 686 | 121 | 44 | 36.3636 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 52.2378 | 37.7049 | 85.0000 | 51.2195 | 23 | 38 | 17 | 3 | 2 | 66.6667 | |
| hfeng-pmm1 | INDEL | D16_PLUS | map_l100_m0_e0 | het | 89.6047 | 94.7368 | 85.0000 | 95.1338 | 18 | 1 | 17 | 3 | 0 | 0.0000 | |
| jlack-gatk | INDEL | D6_15 | map_l250_m1_e0 | * | 89.4737 | 94.4444 | 85.0000 | 97.2452 | 17 | 1 | 17 | 3 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | D16_PLUS | map_l100_m0_e0 | het | 89.6047 | 94.7368 | 85.0000 | 96.1538 | 18 | 1 | 17 | 3 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | D16_PLUS | map_l100_m0_e0 | het | 89.6047 | 94.7368 | 85.0000 | 95.3271 | 18 | 1 | 17 | 3 | 0 | 0.0000 | |
| mlin-fermikit | INDEL | I1_5 | map_l250_m1_e0 | homalt | 53.1250 | 38.6364 | 85.0000 | 92.5094 | 17 | 27 | 17 | 3 | 3 | 100.0000 | |
| rpoplin-dv42 | INDEL | I1_5 | map_l125_m1_e0 | hetalt | 91.8919 | 100.0000 | 85.0000 | 94.2029 | 17 | 0 | 17 | 3 | 0 | 0.0000 | |
| jmaeng-gatk | INDEL | D16_PLUS | map_l100_m0_e0 | het | 89.6047 | 94.7368 | 85.0000 | 97.3510 | 18 | 1 | 17 | 3 | 0 | 0.0000 | |
| ckim-gatk | INDEL | D16_PLUS | map_l150_m2_e0 | * | 91.8919 | 100.0000 | 85.0000 | 97.7503 | 17 | 0 | 17 | 3 | 0 | 0.0000 | |
| ckim-gatk | INDEL | D16_PLUS | map_l150_m2_e1 | * | 89.4737 | 94.4444 | 85.0000 | 97.7925 | 17 | 1 | 17 | 3 | 0 | 0.0000 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 42.7673 | 28.5714 | 85.0000 | 56.5217 | 10 | 25 | 17 | 3 | 3 | 100.0000 | |
| eyeh-varpipe | INDEL | I6_15 | map_l125_m0_e0 | het | 74.7253 | 66.6667 | 85.0000 | 84.1270 | 6 | 3 | 17 | 3 | 2 | 66.6667 | |
| eyeh-varpipe | INDEL | I6_15 | map_siren | homalt | 86.3666 | 87.7778 | 85.0000 | 74.0821 | 79 | 11 | 102 | 18 | 17 | 94.4444 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 49.1036 | 34.5238 | 85.0000 | 53.9171 | 58 | 110 | 85 | 15 | 15 | 100.0000 | |
| gduggal-snapfb | INDEL | * | map_l125_m2_e0 | hetalt | 76.1978 | 69.0476 | 85.0000 | 95.2719 | 29 | 13 | 17 | 3 | 1 | 33.3333 | |
| gduggal-snapfb | INDEL | * | map_l125_m2_e1 | hetalt | 75.2098 | 67.4419 | 85.0000 | 95.3271 | 29 | 14 | 17 | 3 | 1 | 33.3333 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 31.7757 | 19.5402 | 85.0000 | 99.9795 | 17 | 70 | 17 | 3 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | map_l100_m0_e0 | het | 89.6047 | 94.7368 | 85.0000 | 97.5248 | 18 | 1 | 17 | 3 | 0 | 0.0000 | |
| anovak-vg | INDEL | D16_PLUS | map_l100_m2_e1 | * | 50.6599 | 36.0825 | 85.0000 | 88.3721 | 35 | 62 | 34 | 6 | 5 | 83.3333 | |
| bgallagher-sentieon | INDEL | D16_PLUS | map_l150_m2_e0 | * | 91.8919 | 100.0000 | 85.0000 | 97.0631 | 17 | 0 | 17 | 3 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | map_l150_m2_e1 | * | 89.4737 | 94.4444 | 85.0000 | 97.1098 | 17 | 1 | 17 | 3 | 0 | 0.0000 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 82.0780 | 79.3651 | 84.9829 | 70.4935 | 500 | 130 | 498 | 88 | 77 | 87.5000 | |
| gduggal-snapplat | INDEL | I1_5 | map_l150_m2_e1 | het | 81.4686 | 78.2334 | 84.9829 | 96.0923 | 248 | 69 | 249 | 44 | 1 | 2.2727 | |
| jlack-gatk | INDEL | * | map_l150_m1_e0 | het | 91.0230 | 98.0117 | 84.9647 | 93.0437 | 838 | 17 | 842 | 149 | 6 | 4.0269 | |
| cchapple-custom | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 0.0000 | 0.0000 | 84.9624 | 96.2875 | 0 | 1 | 226 | 40 | 3 | 7.5000 | |
| cchapple-custom | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 0.0000 | 0.0000 | 84.9624 | 96.2875 | 0 | 1 | 226 | 40 | 3 | 7.5000 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 90.1316 | 95.9720 | 84.9612 | 56.9426 | 548 | 23 | 548 | 97 | 95 | 97.9381 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 86.9083 | 88.9474 | 84.9606 | 72.8067 | 1183 | 147 | 1401 | 248 | 226 | 91.1290 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 81.9603 | 79.1667 | 84.9582 | 78.0562 | 304 | 80 | 305 | 54 | 43 | 79.6296 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m1_e0 | het | 91.4439 | 99.0074 | 84.9539 | 88.4423 | 1197 | 12 | 1197 | 212 | 63 | 29.7170 | |
| gduggal-bwavard | INDEL | * | map_l100_m0_e0 | * | 89.2130 | 93.9219 | 84.9537 | 89.1607 | 1468 | 95 | 1468 | 260 | 67 | 25.7692 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 90.5202 | 96.8720 | 84.9501 | 59.2685 | 3066 | 99 | 3065 | 543 | 542 | 99.8158 | |
| gduggal-snapfb | INDEL | D1_5 | HG002complexvar | hetalt | 78.9505 | 73.7426 | 84.9498 | 82.4839 | 997 | 355 | 508 | 90 | 54 | 60.0000 | |
| ciseli-custom | SNP | tv | map_l125_m2_e1 | * | 79.4183 | 74.5632 | 84.9497 | 78.4301 | 12420 | 4237 | 12412 | 2199 | 540 | 24.5566 | |
| mlin-fermikit | SNP | ti | map_l125_m0_e0 | * | 52.3097 | 37.7919 | 84.9392 | 57.8951 | 4823 | 7939 | 4822 | 855 | 764 | 89.3567 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 87.7527 | 90.7596 | 84.9385 | 91.1277 | 1601 | 163 | 1658 | 294 | 16 | 5.4422 | |
| mlin-fermikit | SNP | ti | map_l250_m2_e1 | * | 48.6646 | 34.1017 | 84.9362 | 80.0607 | 1731 | 3345 | 1731 | 307 | 262 | 85.3420 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 49.6249 | 35.0531 | 84.9315 | 68.9362 | 231 | 428 | 62 | 11 | 11 | 100.0000 | |
| gduggal-bwafb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 49.6249 | 35.0531 | 84.9315 | 68.9362 | 231 | 428 | 62 | 11 | 11 | 100.0000 | |
| mlin-fermikit | INDEL | I6_15 | * | het | 88.6098 | 92.6243 | 84.9289 | 50.1273 | 9293 | 740 | 9315 | 1653 | 1640 | 99.2136 | |