PrecisionFDA
Truth Challenge
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
50701-50750 / 86044 show all | |||||||||||||||
| ckim-gatk | INDEL | D1_5 | map_l250_m1_e0 | * | 91.5531 | 98.2456 | 85.7143 | 96.6701 | 168 | 3 | 168 | 28 | 1 | 3.5714 | |
| ckim-gatk | INDEL | D1_5 | map_l250_m1_e0 | het | 88.8000 | 100.0000 | 79.8561 | 97.0394 | 111 | 0 | 111 | 28 | 1 | 3.5714 | |
| ckim-gatk | INDEL | D1_5 | map_l250_m2_e0 | * | 92.1120 | 98.3696 | 86.6029 | 96.8600 | 181 | 3 | 181 | 28 | 1 | 3.5714 | |
| ckim-gatk | INDEL | D1_5 | map_l250_m2_e0 | het | 89.6296 | 100.0000 | 81.2081 | 97.1866 | 121 | 0 | 121 | 28 | 1 | 3.5714 | |
| ckim-gatk | INDEL | D1_5 | map_l250_m2_e1 | * | 92.1519 | 98.3784 | 86.6667 | 96.9213 | 182 | 3 | 182 | 28 | 1 | 3.5714 | |
| ckim-gatk | INDEL | D1_5 | map_l250_m2_e1 | het | 89.7059 | 100.0000 | 81.3333 | 97.2355 | 122 | 0 | 122 | 28 | 1 | 3.5714 | |
| eyeh-varpipe | SNP | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 51.4286 | 64.2857 | 42.8571 | 93.8442 | 27 | 15 | 21 | 28 | 1 | 3.5714 | |
| ckim-vqsr | SNP | tv | map_siren | * | 82.2625 | 70.1676 | 99.3954 | 75.7194 | 32228 | 13702 | 32221 | 196 | 7 | 3.5714 | |
| jlack-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.4079 | 99.8008 | 97.0534 | 66.9969 | 17533 | 35 | 17523 | 532 | 19 | 3.5714 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.2911 | 99.8620 | 98.7267 | 65.1671 | 2171 | 3 | 2171 | 28 | 1 | 3.5714 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.9286 | 99.8558 | 98.0184 | 66.5562 | 1385 | 2 | 1385 | 28 | 1 | 3.5714 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.0024 | 99.9306 | 98.0913 | 69.9262 | 1439 | 1 | 1439 | 28 | 1 | 3.5714 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 98.4914 | 100.0000 | 97.0276 | 71.0154 | 914 | 0 | 914 | 28 | 1 | 3.5714 | |
| hfeng-pmm3 | SNP | * | map_l250_m0_e0 | het | 98.0731 | 98.0080 | 98.1383 | 92.9489 | 1476 | 30 | 1476 | 28 | 1 | 3.5714 | |
| jpowers-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 98.1120 | 99.2341 | 97.0149 | 76.5207 | 907 | 7 | 910 | 28 | 1 | 3.5714 | |
| asubramanian-gatk | INDEL | D1_5 | map_l150_m0_e0 | het | 88.8889 | 91.0891 | 86.7925 | 93.8746 | 184 | 18 | 184 | 28 | 1 | 3.5714 | |
| ciseli-custom | SNP | tv | map_l100_m2_e0 | het | 79.2677 | 74.3804 | 84.8423 | 77.0207 | 11735 | 4042 | 11732 | 2096 | 75 | 3.5782 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 84.9187 | 82.8004 | 87.1483 | 74.4451 | 3211 | 667 | 3221 | 475 | 17 | 3.5790 | |
| jlack-gatk | SNP | * | * | * | 99.7200 | 99.9393 | 99.5016 | 23.6335 | 3052765 | 1854 | 3052612 | 15290 | 548 | 3.5840 | |
| ckim-gatk | SNP | tv | map_l150_m2_e1 | * | 80.0038 | 68.1273 | 96.8955 | 89.4103 | 7836 | 3666 | 7834 | 251 | 9 | 3.5857 | |
| mlin-fermikit | SNP | * | map_l125_m1_e0 | het | 60.7541 | 43.9737 | 98.2445 | 60.8741 | 12485 | 15907 | 12480 | 223 | 8 | 3.5874 | |
| jmaeng-gatk | SNP | * | * | * | 99.6144 | 99.4608 | 99.7686 | 23.7289 | 3038147 | 16472 | 3038001 | 7046 | 253 | 3.5907 | |
| gduggal-snapvard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 82.8968 | 94.7123 | 73.7023 | 85.2096 | 6305 | 352 | 6233 | 2224 | 80 | 3.5971 | |
| ckim-gatk | SNP | tv | map_l150_m2_e1 | het | 84.0437 | 74.9456 | 95.6560 | 90.8674 | 5507 | 1841 | 5505 | 250 | 9 | 3.6000 | |
| 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 | |
| jlack-gatk | INDEL | * | map_l150_m0_e0 | * | 91.3832 | 97.6654 | 85.8603 | 94.2048 | 502 | 12 | 504 | 83 | 3 | 3.6145 | |
| raldana-dualsentieon | SNP | * | map_l125_m1_e0 | * | 99.1433 | 99.2014 | 99.0854 | 69.5094 | 44965 | 362 | 44959 | 415 | 15 | 3.6145 | |
| gduggal-snapvard | SNP | tv | map_l250_m1_e0 | * | 84.2656 | 95.6932 | 75.2762 | 90.8080 | 2533 | 114 | 2521 | 828 | 30 | 3.6232 | |
| ckim-vqsr | SNP | tv | * | het | 99.3645 | 98.9162 | 99.8170 | 31.1430 | 585283 | 6413 | 585211 | 1073 | 39 | 3.6347 | |
| raldana-dualsentieon | SNP | ti | map_l150_m1_e0 | * | 98.9223 | 98.9600 | 98.8846 | 73.7335 | 19507 | 205 | 19503 | 220 | 8 | 3.6364 | |
| gduggal-snapplat | INDEL | I1_5 | map_l150_m2_e0 | * | 82.6518 | 77.8420 | 88.0952 | 95.5115 | 404 | 115 | 407 | 55 | 2 | 3.6364 | |
| jmaeng-gatk | SNP | tv | map_l125_m2_e1 | * | 84.0047 | 74.0950 | 96.9745 | 86.2788 | 12342 | 4315 | 12340 | 385 | 14 | 3.6364 | |
| jmaeng-gatk | SNP | tv | map_l250_m1_e0 | * | 67.4516 | 51.9456 | 96.1538 | 96.4328 | 1375 | 1272 | 1375 | 55 | 2 | 3.6364 | |
| gduggal-snapvard | SNP | tv | map_l250_m2_e1 | * | 84.9786 | 95.5761 | 76.4966 | 91.4134 | 2787 | 129 | 2773 | 852 | 31 | 3.6385 | |
| jlack-gatk | SNP | ti | * | het | 99.6581 | 99.9316 | 99.3861 | 24.9292 | 1281014 | 877 | 1280960 | 7913 | 288 | 3.6396 | |
| gduggal-snapvard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 75.3471 | 93.5728 | 63.0638 | 89.0931 | 2475 | 170 | 2433 | 1425 | 52 | 3.6491 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 78.1790 | 97.7444 | 65.1399 | 76.7730 | 260 | 6 | 256 | 137 | 5 | 3.6496 | |
| ckim-vqsr | SNP | * | map_l100_m2_e1 | het | 85.4225 | 75.1205 | 98.9994 | 84.8723 | 35230 | 11668 | 35222 | 356 | 13 | 3.6517 | |
| raldana-dualsentieon | SNP | tv | map_siren | * | 99.5658 | 99.6081 | 99.5235 | 57.2670 | 45750 | 180 | 45742 | 219 | 8 | 3.6530 | |
| gduggal-snapplat | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 84.5678 | 88.4131 | 81.0431 | 88.8392 | 4212 | 552 | 4211 | 985 | 36 | 3.6548 | |
| ciseli-custom | SNP | ti | HG002compoundhet | het | 71.3901 | 79.1057 | 65.0459 | 46.7631 | 7519 | 1986 | 7585 | 4076 | 149 | 3.6555 | |
| gduggal-snapvard | SNP | tv | map_l250_m2_e0 | * | 84.9127 | 95.5933 | 76.3788 | 91.3348 | 2755 | 127 | 2742 | 848 | 31 | 3.6557 | |
| bgallagher-sentieon | SNP | ti | segdup | * | 99.5103 | 99.8567 | 99.1663 | 89.5899 | 19509 | 28 | 19507 | 164 | 6 | 3.6585 | |
| ckim-vqsr | SNP | * | map_l100_m2_e0 | het | 85.3365 | 74.9930 | 98.9898 | 84.8848 | 34796 | 11603 | 34788 | 355 | 13 | 3.6620 | |
| gduggal-bwavard | SNP | * | map_l150_m0_e0 | het | 89.4308 | 97.6574 | 82.4825 | 88.0388 | 7754 | 186 | 7675 | 1630 | 60 | 3.6810 | |
| eyeh-varpipe | SNP | ti | map_l100_m0_e0 | het | 98.7795 | 99.5137 | 98.0561 | 74.4857 | 13915 | 68 | 13670 | 271 | 10 | 3.6900 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 96.0835 | 99.8396 | 92.5998 | 68.1347 | 2490 | 4 | 2365 | 189 | 7 | 3.7037 | |
| ciseli-custom | SNP | ti | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 42.5532 | 100.0000 | 27.0270 | 90.7500 | 6 | 0 | 10 | 27 | 1 | 3.7037 | |
| cchapple-custom | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 0.0000 | 0.0000 | 77.8689 | 96.2531 | 0 | 0 | 95 | 27 | 1 | 3.7037 | |