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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
401-450 / 86044 show all | |||||||||||||||
| gduggal-snapfb | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 88.3624 | 85.5319 | 91.3867 | 71.3799 | 80784 | 13665 | 85516 | 8060 | 4292 | 53.2506 | |
| ckim-vqsr | SNP | ti | map_l125_m2_e1 | * | 71.0090 | 55.3306 | 99.0860 | 88.2132 | 16914 | 13655 | 16912 | 156 | 5 | 3.2051 | |
| eyeh-varpipe | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 87.5783 | 85.5583 | 89.6959 | 70.2246 | 80809 | 13640 | 139087 | 15978 | 15625 | 97.7907 | |
| ckim-isaac | SNP | tv | * | homalt | 98.1562 | 96.3855 | 99.9931 | 16.5795 | 363492 | 13631 | 363515 | 25 | 18 | 72.0000 | |
| gduggal-bwaplat | SNP | ti | map_l100_m2_e0 | * | 83.6206 | 72.1656 | 99.3982 | 81.0322 | 35333 | 13628 | 35344 | 214 | 67 | 31.3084 | |
| gduggal-bwaplat | SNP | ti | map_l100_m1_e0 | * | 83.2803 | 71.6572 | 99.4040 | 79.8206 | 34346 | 13585 | 34357 | 206 | 64 | 31.0680 | |
| ckim-vqsr | SNP | ti | map_l125_m2_e0 | * | 70.8577 | 55.1491 | 99.0796 | 88.2228 | 16687 | 13571 | 16685 | 155 | 5 | 3.2258 | |
| eyeh-varpipe | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 71.2051 | 68.6858 | 73.9162 | 57.7097 | 29765 | 13570 | 41841 | 14765 | 14397 | 97.5076 | |
| gduggal-snapvard | SNP | ti | * | het | 98.9307 | 98.9471 | 98.9142 | 25.7701 | 1268399 | 13497 | 1263991 | 13875 | 2046 | 14.7459 | |
| ckim-isaac | SNP | * | map_l100_m0_e0 | * | 74.0949 | 58.9233 | 99.7886 | 67.9602 | 19351 | 13490 | 19354 | 41 | 9 | 21.9512 | |
| gduggal-snapvard | INDEL | I6_15 | * | * | 50.7754 | 45.6827 | 57.1459 | 41.2412 | 11338 | 13481 | 13483 | 10111 | 8109 | 80.1998 | |
| gduggal-snapplat | SNP | * | HG002complexvar | het | 97.4346 | 97.1046 | 97.7668 | 23.9217 | 452022 | 13478 | 453020 | 10348 | 1516 | 14.6502 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 0.0000 | 4.0479 | 0.0000 | 0.0000 | 568 | 13464 | 0 | 0 | 0 | ||
| ciseli-custom | SNP | * | map_l100_m2_e1 | * | 85.2411 | 82.0102 | 88.7370 | 71.8319 | 61292 | 13445 | 61099 | 7755 | 2048 | 26.4088 | |
| gduggal-bwaplat | SNP | * | map_siren | homalt | 86.1632 | 75.7053 | 99.9736 | 58.6738 | 41756 | 13400 | 41721 | 11 | 9 | 81.8182 | |
| ckim-vqsr | SNP | ti | map_l125_m1_e0 | * | 70.1902 | 54.3480 | 99.0678 | 87.5048 | 15943 | 13392 | 15941 | 150 | 4 | 2.6667 | |
| ciseli-custom | SNP | * | map_l100_m2_e0 | * | 85.1771 | 81.9318 | 88.6900 | 71.8362 | 60600 | 13364 | 60413 | 7704 | 2033 | 26.3889 | |
| ckim-gatk | SNP | * | map_l100_m2_e1 | * | 89.5170 | 82.2096 | 98.2503 | 79.5686 | 61441 | 13296 | 61430 | 1094 | 86 | 7.8611 | |
| jmaeng-gatk | SNP | * | map_l100_m2_e1 | * | 89.5016 | 82.2404 | 98.1693 | 79.7702 | 61464 | 13273 | 61453 | 1146 | 79 | 6.8935 | |
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 65.2231 | 63.7325 | 66.7851 | 42.6875 | 23321 | 13271 | 40773 | 20278 | 18291 | 90.2012 | |
| ckim-gatk | SNP | * | map_l100_m2_e0 | * | 89.4294 | 82.0710 | 98.2373 | 79.5869 | 60703 | 13261 | 60692 | 1089 | 86 | 7.8972 | |
| ciseli-custom | SNP | * | map_l100_m1_e0 | * | 84.9995 | 81.6845 | 88.5950 | 70.0712 | 59142 | 13261 | 58960 | 7590 | 2012 | 26.5086 | |
| jmaeng-gatk | SNP | * | map_l100_m2_e0 | * | 89.4136 | 82.0994 | 98.1585 | 79.7900 | 60724 | 13240 | 60713 | 1139 | 79 | 6.9359 | |
| qzeng-custom | SNP | ti | map_siren | * | 92.5421 | 86.8188 | 99.0732 | 61.8902 | 87127 | 13228 | 86370 | 808 | 570 | 70.5446 | |
| ckim-gatk | SNP | * | map_l100_m1_e0 | * | 89.2398 | 81.7300 | 98.2693 | 78.3708 | 59175 | 13228 | 59164 | 1042 | 84 | 8.0614 | |
| jmaeng-gatk | SNP | * | map_l100_m1_e0 | * | 89.2166 | 81.7563 | 98.1753 | 78.5878 | 59194 | 13209 | 59183 | 1100 | 78 | 7.0909 | |
| ciseli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 0.0000 | 4.0395 | 0.0000 | 0.0000 | 556 | 13208 | 0 | 0 | 0 | ||
| mlin-fermikit | SNP | ti | map_l100_m2_e1 | het | 72.5397 | 57.3547 | 98.6610 | 56.4877 | 17757 | 13203 | 17757 | 241 | 9 | 3.7344 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 42.4269 | 27.3328 | 94.7531 | 66.0231 | 4965 | 13200 | 5219 | 289 | 255 | 88.2353 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 42.4269 | 27.3328 | 94.7531 | 66.0231 | 4965 | 13200 | 5219 | 289 | 255 | 88.2353 | |
| ckim-isaac | SNP | ti | map_siren | het | 88.1134 | 78.8433 | 99.8538 | 52.2793 | 49184 | 13198 | 49191 | 72 | 6 | 8.3333 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 79.4183 | 79.5592 | 79.2778 | 75.7467 | 51260 | 13170 | 51089 | 13354 | 8419 | 63.0448 | |
| mlin-fermikit | SNP | ti | map_l100_m2_e0 | het | 72.2999 | 57.0570 | 98.6561 | 56.4180 | 17472 | 13150 | 17472 | 238 | 9 | 3.7815 | |
| gduggal-snapvard | INDEL | * | * | het | 84.4835 | 93.2561 | 77.2195 | 60.6809 | 181038 | 13092 | 228131 | 67301 | 50370 | 74.8429 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 45.9726 | 41.2090 | 51.9814 | 51.1983 | 9169 | 13081 | 9156 | 8458 | 8386 | 99.1487 | |
| mlin-fermikit | SNP | ti | map_l100_m1_e0 | het | 71.7393 | 56.3489 | 98.6955 | 52.5376 | 16872 | 13070 | 16872 | 223 | 9 | 4.0359 | |
| gduggal-snapvard | INDEL | D1_5 | * | * | 87.8248 | 91.1601 | 84.7249 | 55.7284 | 133771 | 12972 | 160064 | 28858 | 22853 | 79.1912 | |
| anovak-vg | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 81.5683 | 79.9506 | 83.2528 | 70.9561 | 51513 | 12918 | 52192 | 10499 | 7538 | 71.7973 | |
| gduggal-snapvard | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 73.0618 | 58.0378 | 98.5812 | 63.1306 | 17853 | 12908 | 28349 | 408 | 382 | 93.6275 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 42.1139 | 37.4782 | 48.0583 | 42.5126 | 7719 | 12877 | 7710 | 8333 | 8271 | 99.2560 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 81.2482 | 70.2896 | 96.2549 | 70.8872 | 30460 | 12875 | 30456 | 1185 | 636 | 53.6709 | |
| ciseli-custom | SNP | ti | HG002complexvar | het | 96.3296 | 95.9112 | 96.7516 | 18.3708 | 301896 | 12870 | 299422 | 10053 | 353 | 3.5114 | |
| asubramanian-gatk | SNP | * | map_l125_m2_e1 | homalt | 42.1801 | 26.7283 | 99.9787 | 88.0838 | 4686 | 12846 | 4686 | 1 | 0 | 0.0000 | |
| mlin-fermikit | SNP | tv | map_siren | * | 81.3085 | 72.1446 | 93.1393 | 50.3116 | 33136 | 12794 | 33125 | 2440 | 2002 | 82.0492 | |
| asubramanian-gatk | SNP | * | map_l125_m2_e0 | homalt | 41.9933 | 26.5784 | 99.9784 | 88.1315 | 4618 | 12757 | 4618 | 1 | 0 | 0.0000 | |
| gduggal-bwaplat | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 83.8912 | 73.6757 | 97.3956 | 82.4238 | 35564 | 12707 | 35564 | 951 | 276 | 29.0221 | |
| anovak-vg | INDEL | I1_5 | HG002complexvar | het | 44.4856 | 30.2381 | 84.1220 | 66.7223 | 5500 | 12689 | 6204 | 1171 | 683 | 58.3262 | |
| asubramanian-gatk | SNP | tv | * | het | 98.8211 | 97.8557 | 99.8057 | 26.7081 | 579008 | 12688 | 578944 | 1127 | 42 | 3.7267 | |
| ciseli-custom | SNP | tv | * | * | 96.5740 | 98.6920 | 94.5451 | 25.2127 | 957014 | 12684 | 954909 | 55095 | 4019 | 7.2947 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 88.4632 | 80.3154 | 98.4508 | 79.5350 | 51748 | 12683 | 51729 | 814 | 499 | 61.3022 | |