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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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84501-84550 / 86044 show all | |||||||||||||||
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 50.1574 | 67.0715 | 40.0560 | 49.5050 | 497 | 244 | 1573 | 2354 | 1678 | 71.2829 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 59.3370 | 47.9747 | 77.7515 | 66.6856 | 5697 | 6178 | 8230 | 2355 | 819 | 34.7771 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 38.8587 | 37.6192 | 40.1826 | 50.2147 | 907 | 1504 | 1584 | 2358 | 1680 | 71.2468 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 70.9699 | 75.4662 | 66.9793 | 63.9738 | 4411 | 1434 | 4785 | 2359 | 1346 | 57.0581 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 70.9699 | 75.4662 | 66.9793 | 63.9738 | 4411 | 1434 | 4785 | 2359 | 1346 | 57.0581 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 82.6766 | 79.8823 | 85.6735 | 55.5568 | 14116 | 3555 | 14119 | 2361 | 2322 | 98.3482 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 82.6766 | 79.8823 | 85.6735 | 55.5568 | 14116 | 3555 | 14119 | 2361 | 2322 | 98.3482 | |
| ciseli-custom | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 58.2603 | 63.0693 | 54.1327 | 69.0970 | 2548 | 1492 | 2790 | 2364 | 1096 | 46.3621 | |
| ghariani-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 76.4899 | 74.2821 | 78.8329 | 50.1539 | 8821 | 3054 | 8808 | 2365 | 2266 | 95.8140 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 89.0249 | 97.7996 | 81.6952 | 39.8894 | 10178 | 229 | 10564 | 2367 | 2280 | 96.3245 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 81.6774 | 94.4237 | 71.9631 | 77.4935 | 6062 | 358 | 6078 | 2368 | 2066 | 87.2466 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 81.6774 | 94.4237 | 71.9631 | 77.4935 | 6062 | 358 | 6078 | 2368 | 2066 | 87.2466 | |
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 83.8511 | 96.7311 | 73.9980 | 86.2278 | 6658 | 225 | 6739 | 2368 | 15 | 0.6334 | |
| ciseli-custom | INDEL | I1_5 | HG002complexvar | het | 88.5454 | 89.7735 | 87.3504 | 57.1664 | 16328 | 1860 | 16352 | 2368 | 1692 | 71.4527 | |
| gduggal-snapvard | SNP | tv | map_siren | * | 95.8840 | 96.8735 | 94.9146 | 68.0322 | 44494 | 1436 | 44271 | 2372 | 211 | 8.8955 | |
| mlin-fermikit | SNP | * | map_l150_m2_e1 | * | 57.9744 | 43.8280 | 85.6051 | 66.1929 | 14117 | 18093 | 14112 | 2373 | 2083 | 87.7792 | |
| ciseli-custom | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 69.5898 | 94.9602 | 54.9176 | 73.3767 | 2864 | 152 | 2898 | 2379 | 40 | 1.6814 | |
| ciseli-custom | SNP | * | map_l100_m2_e0 | homalt | 90.4763 | 89.7867 | 91.1766 | 62.8157 | 24712 | 2811 | 24604 | 2381 | 1867 | 78.4124 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 42.8855 | 43.0211 | 42.7507 | 47.9409 | 937 | 1241 | 1778 | 2381 | 1894 | 79.5464 | |
| gduggal-bwafb | INDEL | * | * | het | 97.2465 | 95.6571 | 98.8897 | 54.7010 | 185702 | 8431 | 212773 | 2389 | 1710 | 71.5781 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 79.2090 | 80.0667 | 78.3696 | 91.0972 | 8648 | 2153 | 8681 | 2396 | 141 | 5.8848 | |
| ciseli-custom | SNP | * | map_l100_m2_e1 | homalt | 90.5022 | 89.8151 | 91.2000 | 62.7951 | 24965 | 2831 | 24852 | 2398 | 1881 | 78.4404 | |
| ckim-isaac | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 94.7847 | 94.6676 | 94.9020 | 63.1937 | 45697 | 2574 | 44659 | 2399 | 1704 | 71.0296 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 86.1593 | 93.2312 | 80.0845 | 46.3972 | 5661 | 411 | 9663 | 2403 | 2342 | 97.4615 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 80.3927 | 81.2870 | 79.5178 | 59.9939 | 9335 | 2149 | 9333 | 2404 | 2119 | 88.1448 | |
| gduggal-bwaplat | SNP | tv | HG002complexvar | * | 97.3488 | 95.7603 | 98.9909 | 25.1801 | 235716 | 10436 | 235930 | 2405 | 362 | 15.0520 | |
| gduggal-snapfb | SNP | * | map_siren | het | 98.1134 | 98.8438 | 97.3936 | 60.3479 | 89939 | 1052 | 89942 | 2407 | 760 | 31.5746 | |
| ckim-gatk | INDEL | * | * | * | 99.2271 | 99.1551 | 99.2992 | 60.7185 | 341631 | 2911 | 341492 | 2410 | 1553 | 64.4398 | |
| jpowers-varprowl | INDEL | * | HG002compoundhet | homalt | 33.5403 | 91.1079 | 20.5534 | 62.6200 | 625 | 61 | 624 | 2412 | 2157 | 89.4279 | |
| ghariani-varprowl | SNP | * | map_siren | het | 98.3861 | 99.3911 | 97.4013 | 64.9618 | 90437 | 554 | 90440 | 2413 | 303 | 12.5570 | |
| gduggal-bwavard | SNP | ti | map_siren | het | 96.4374 | 96.7603 | 96.1167 | 68.4382 | 60361 | 2021 | 59849 | 2418 | 250 | 10.3391 | |
| mlin-fermikit | SNP | ti | map_l100_m1_e0 | homalt | 75.0582 | 68.1626 | 83.5061 | 48.1080 | 12242 | 5718 | 12242 | 2418 | 2328 | 96.2779 | |
| jlack-gatk | SNP | * | map_l150_m1_e0 | het | 93.5301 | 98.8559 | 88.7489 | 85.6678 | 19095 | 221 | 19089 | 2420 | 175 | 7.2314 | |
| ghariani-varprowl | SNP | * | HG002compoundhet | homalt | 89.8311 | 99.8331 | 81.6508 | 42.6198 | 10764 | 18 | 10773 | 2421 | 2004 | 82.7757 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 89.5433 | 87.3487 | 91.8510 | 85.8019 | 27203 | 3940 | 27288 | 2421 | 244 | 10.0785 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 89.5433 | 87.3487 | 91.8510 | 85.8019 | 27203 | 3940 | 27288 | 2421 | 244 | 10.0785 | |
| rpoplin-dv42 | INDEL | * | * | het | 99.0459 | 99.3340 | 98.7595 | 59.2937 | 192840 | 1293 | 192749 | 2421 | 2250 | 92.9368 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 65.3933 | 98.2278 | 49.0105 | 39.1883 | 2328 | 42 | 2328 | 2422 | 2406 | 99.3394 | |
| eyeh-varpipe | SNP | tv | map_siren | het | 95.7583 | 99.7903 | 92.0396 | 63.5402 | 28549 | 60 | 28096 | 2430 | 18 | 0.7407 | |
| ciseli-custom | INDEL | I6_15 | HG002compoundhet | homalt | 0.8094 | 32.2581 | 0.4098 | 28.2142 | 10 | 21 | 10 | 2430 | 2370 | 97.5309 | |
| ghariani-varprowl | INDEL | * | HG002compoundhet | homalt | 33.4304 | 91.1079 | 20.4709 | 62.9558 | 625 | 61 | 626 | 2432 | 2127 | 87.4589 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 61.8393 | 51.5519 | 77.2561 | 71.5347 | 8288 | 7789 | 8261 | 2432 | 2302 | 94.6546 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 61.8393 | 51.5519 | 77.2561 | 71.5347 | 8288 | 7789 | 8261 | 2432 | 2302 | 94.6546 | |
| eyeh-varpipe | INDEL | I6_15 | HG002compoundhet | * | 36.3679 | 28.3500 | 50.7094 | 30.4777 | 2488 | 6288 | 2502 | 2432 | 2425 | 99.7122 | |
| gduggal-bwaplat | SNP | ti | HG002compoundhet | het | 83.6361 | 90.0158 | 78.1008 | 46.8217 | 8556 | 949 | 8677 | 2433 | 181 | 7.4394 | |
| mlin-fermikit | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 72.4419 | 70.6939 | 74.2785 | 64.5876 | 7121 | 2952 | 7026 | 2433 | 2324 | 95.5199 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 91.9743 | 92.1019 | 91.8470 | 57.2556 | 26028 | 2232 | 27420 | 2434 | 1757 | 72.1857 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 53.2015 | 46.3732 | 62.3880 | 36.5667 | 748 | 865 | 4039 | 2435 | 1935 | 79.4661 | |
| mlin-fermikit | INDEL | D6_15 | * | * | 87.9258 | 85.7734 | 90.1891 | 52.9541 | 22380 | 3712 | 22421 | 2439 | 2392 | 98.0730 | |
| mlin-fermikit | SNP | tv | map_siren | * | 81.3085 | 72.1446 | 93.1393 | 50.3116 | 33136 | 12794 | 33125 | 2440 | 2002 | 82.0492 | |