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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
20001-20050 / 86044 show all | |||||||||||||||
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.2054 | 98.6910 | 99.7252 | 56.8874 | 19602 | 260 | 19598 | 54 | 35 | 64.8148 | |
| gduggal-snapvard | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 48.6618 | 55.8168 | 43.1327 | 62.9167 | 2255 | 1785 | 5053 | 6662 | 4317 | 64.8004 | |
| gduggal-snapvard | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 38.5774 | 33.9720 | 44.6273 | 63.2598 | 3422 | 6651 | 5395 | 6694 | 4337 | 64.7894 | |
| ndellapenna-hhga | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5085 | 97.7714 | 99.2568 | 64.1000 | 9476 | 216 | 9482 | 71 | 46 | 64.7887 | |
| eyeh-varpipe | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 0.0000 | 0.0000 | 61.8280 | 95.2210 | 0 | 0 | 115 | 71 | 46 | 64.7887 | |
| eyeh-varpipe | INDEL | C6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 0.0000 | 0.0000 | 61.8280 | 95.2210 | 0 | 0 | 115 | 71 | 46 | 64.7887 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 71.7034 | 76.5182 | 67.4586 | 62.2452 | 3402 | 1044 | 3748 | 1808 | 1171 | 64.7677 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.8438 | 95.8592 | 97.8488 | 71.3186 | 4792 | 207 | 4776 | 105 | 68 | 64.7619 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.8438 | 95.8592 | 97.8488 | 71.3186 | 4792 | 207 | 4776 | 105 | 68 | 64.7619 | |
| rpoplin-dv42 | SNP | ti | map_l150_m2_e0 | het | 99.0005 | 98.8200 | 99.1816 | 75.9652 | 12729 | 152 | 12725 | 105 | 68 | 64.7619 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.6132 | 95.1837 | 98.0864 | 57.9273 | 8004 | 405 | 7996 | 156 | 101 | 64.7436 | |
| jli-custom | INDEL | I1_5 | * | het | 99.6300 | 99.4800 | 99.7804 | 58.4682 | 78630 | 411 | 78600 | 173 | 112 | 64.7399 | |
| ciseli-custom | INDEL | * | map_l125_m2_e1 | * | 67.9362 | 62.5618 | 74.3207 | 90.8519 | 1392 | 833 | 1395 | 482 | 312 | 64.7303 | |
| ciseli-custom | INDEL | * | map_l250_m2_e0 | homalt | 59.5745 | 48.6957 | 76.7123 | 96.9159 | 56 | 59 | 56 | 17 | 11 | 64.7059 | |
| ciseli-custom | INDEL | * | map_l250_m2_e1 | homalt | 60.0000 | 49.1379 | 77.0270 | 96.9384 | 57 | 59 | 57 | 17 | 11 | 64.7059 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 78.8110 | 71.5116 | 87.7698 | 75.9099 | 123 | 49 | 122 | 17 | 11 | 64.7059 | |
| ciseli-custom | SNP | tv | map_l250_m0_e0 | homalt | 73.5751 | 73.5751 | 73.5751 | 93.4487 | 142 | 51 | 142 | 51 | 33 | 64.7059 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.2804 | 98.3316 | 98.2292 | 73.6842 | 943 | 16 | 943 | 17 | 11 | 64.7059 | |
| ckim-gatk | SNP | ti | * | homalt | 99.6240 | 99.2571 | 99.9936 | 16.1503 | 797072 | 5966 | 797063 | 51 | 33 | 64.7059 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 19.8805 | 11.8959 | 60.4651 | 91.9021 | 32 | 237 | 26 | 17 | 11 | 64.7059 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 94.9273 | 92.5764 | 97.4006 | 82.2668 | 636 | 51 | 637 | 17 | 11 | 64.7059 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.4371 | 91.9154 | 99.2394 | 60.4914 | 2217 | 195 | 2218 | 17 | 11 | 64.7059 | |
| raldana-dualsentieon | INDEL | * | map_siren | homalt | 99.3604 | 99.3597 | 99.3611 | 79.7735 | 2638 | 17 | 2644 | 17 | 11 | 64.7059 | |
| mlin-fermikit | INDEL | D6_15 | map_l125_m1_e0 | * | 74.9115 | 68.3761 | 82.8283 | 83.9286 | 80 | 37 | 82 | 17 | 11 | 64.7059 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 84.6414 | 86.8827 | 82.5129 | 86.9736 | 1126 | 170 | 1123 | 238 | 154 | 64.7059 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 96.7182 | 95.3340 | 98.1431 | 70.1548 | 1798 | 88 | 1797 | 34 | 22 | 64.7059 | |
| ltrigg-rtg2 | INDEL | I1_5 | HG002complexvar | * | 99.3818 | 99.0798 | 99.6856 | 52.9504 | 33055 | 307 | 32342 | 102 | 66 | 64.7059 | |
| gduggal-snapvard | INDEL | I16_PLUS | * | homalt | 1.5180 | 0.7687 | 60.0000 | 43.7086 | 12 | 1549 | 51 | 34 | 22 | 64.7059 | |
| gduggal-snapvard | INDEL | I16_PLUS | map_siren | het | 7.6607 | 4.0816 | 62.2222 | 78.3654 | 2 | 47 | 28 | 17 | 11 | 64.7059 | |
| gduggal-snapvard | SNP | tv | map_l100_m2_e0 | homalt | 98.2526 | 96.7441 | 99.8089 | 63.7260 | 8914 | 300 | 8881 | 17 | 11 | 64.7059 | |
| gduggal-snapvard | SNP | tv | map_l100_m2_e1 | homalt | 98.2305 | 96.6996 | 99.8105 | 63.7425 | 8995 | 307 | 8956 | 17 | 11 | 64.7059 | |
| eyeh-varpipe | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 0.0000 | 0.0000 | 24.4444 | 96.6518 | 0 | 0 | 11 | 34 | 22 | 64.7059 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.3261 | 97.7936 | 98.8644 | 77.1834 | 1507 | 34 | 1480 | 17 | 11 | 64.7059 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.4981 | 99.1184 | 97.8856 | 89.2499 | 787 | 7 | 787 | 17 | 11 | 64.7059 | |
| anovak-vg | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 44.8785 | 34.5273 | 64.0937 | 56.3014 | 588 | 1115 | 1669 | 935 | 605 | 64.7059 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 87.7794 | 88.9764 | 86.6142 | 67.2680 | 113 | 14 | 110 | 17 | 11 | 64.7059 | |
| gduggal-bwavard | INDEL | * | HG002complexvar | homalt | 95.0919 | 90.9942 | 99.5761 | 40.5691 | 24593 | 2434 | 23958 | 102 | 66 | 64.7059 | |
| gduggal-bwavard | INDEL | D1_5 | HG002complexvar | homalt | 96.6460 | 93.8290 | 99.6373 | 42.9597 | 9944 | 654 | 9340 | 34 | 22 | 64.7059 | |
| gduggal-bwavard | INDEL | I1_5 | * | homalt | 95.1435 | 90.7626 | 99.9687 | 33.2973 | 54846 | 5582 | 54343 | 17 | 11 | 64.7059 | |
| ciseli-custom | INDEL | * | map_l125_m1_e0 | * | 67.4524 | 62.0788 | 73.8444 | 90.3002 | 1308 | 799 | 1310 | 464 | 300 | 64.6552 | |
| rpoplin-dv42 | SNP | * | map_l150_m1_e0 | * | 99.0457 | 98.8533 | 99.2389 | 73.2840 | 30258 | 351 | 30252 | 232 | 150 | 64.6552 | |
| anovak-vg | INDEL | D1_5 | HG002compoundhet | het | 54.0229 | 57.5810 | 50.8790 | 62.2806 | 995 | 733 | 4428 | 4275 | 2764 | 64.6550 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2219 | 99.3862 | 99.0582 | 74.4553 | 33032 | 204 | 33027 | 314 | 203 | 64.6497 | |
| jpowers-varprowl | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 98.8278 | 100.0000 | 97.6827 | 39.6904 | 2738 | 0 | 2740 | 65 | 42 | 64.6154 | |
| anovak-vg | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 33.1255 | 25.5937 | 46.9388 | 67.3333 | 97 | 282 | 115 | 130 | 84 | 64.6154 | |
| anovak-vg | INDEL | I6_15 | HG002complexvar | het | 40.0214 | 28.2378 | 68.6825 | 52.4803 | 665 | 1690 | 954 | 435 | 281 | 64.5977 | |
| ciseli-custom | INDEL | * | map_l125_m2_e0 | * | 67.7061 | 62.3406 | 74.0821 | 90.8144 | 1369 | 827 | 1372 | 480 | 310 | 64.5833 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 96.8519 | 94.5071 | 99.3160 | 27.2218 | 6951 | 404 | 6970 | 48 | 31 | 64.5833 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 11.1206 | 7.0388 | 26.4706 | 75.6646 | 58 | 766 | 63 | 175 | 113 | 64.5714 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 16.8844 | 12.6126 | 25.5319 | 75.5463 | 56 | 388 | 60 | 175 | 113 | 64.5714 | |