PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
2401-2450 / 86044 show all | |||||||||||||||
| gduggal-snapplat | SNP | ti | map_l125_m2_e0 | * | 94.3195 | 92.4218 | 96.2968 | 81.1125 | 27965 | 2293 | 27980 | 1076 | 588 | 54.6468 | |
| hfeng-pmm2 | INDEL | * | * | homalt | 99.6594 | 99.8043 | 99.5149 | 55.8756 | 124927 | 245 | 124935 | 609 | 588 | 96.5517 | |
| raldana-dualsentieon | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.6413 | 97.9883 | 99.3029 | 72.0487 | 92549 | 1900 | 92457 | 649 | 588 | 90.6009 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.6451 | 97.4107 | 97.8807 | 69.5745 | 5944 | 158 | 34593 | 749 | 587 | 78.3712 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 43.4757 | 29.7973 | 80.3688 | 59.6728 | 2837 | 6684 | 2833 | 692 | 587 | 84.8266 | |
| gduggal-snapplat | SNP | ti | map_l125_m1_e0 | * | 94.1774 | 92.2277 | 96.2113 | 79.7747 | 27055 | 2280 | 27070 | 1066 | 586 | 54.9719 | |
| mlin-fermikit | SNP | tv | HG002compoundhet | homalt | 90.3108 | 98.4357 | 83.4250 | 51.0104 | 3335 | 53 | 3337 | 663 | 585 | 88.2353 | |
| anovak-vg | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 23.1772 | 16.4208 | 39.3809 | 42.5111 | 345 | 1756 | 458 | 705 | 585 | 82.9787 | |
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 53.0813 | 57.1912 | 49.5224 | 53.3105 | 676 | 506 | 674 | 687 | 585 | 85.1528 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 88.9611 | 96.9686 | 82.1752 | 61.2865 | 2719 | 85 | 2720 | 590 | 583 | 98.8136 | |
| qzeng-custom | INDEL | I6_15 | * | het | 91.4351 | 95.6444 | 87.5806 | 52.1449 | 9596 | 437 | 11812 | 1675 | 583 | 34.8060 | |
| ckim-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9696 | 98.6829 | 99.2581 | 73.7654 | 93205 | 1244 | 93112 | 696 | 583 | 83.7644 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 91.8499 | 88.8266 | 95.0863 | 43.5099 | 14254 | 1793 | 14165 | 732 | 583 | 79.6448 | |
| egarrison-hhga | INDEL | D1_5 | HG002complexvar | * | 97.4539 | 97.1695 | 97.7400 | 55.3894 | 31789 | 926 | 31787 | 735 | 582 | 79.1837 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.2904 | 99.2602 | 97.3394 | 75.4562 | 21737 | 162 | 21732 | 594 | 582 | 97.9798 | |
| astatham-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.1675 | 99.0429 | 99.2924 | 73.5960 | 93545 | 904 | 93452 | 666 | 582 | 87.3874 | |
| ckim-dragen | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.9650 | 99.8245 | 98.1202 | 75.4285 | 30707 | 54 | 30692 | 588 | 582 | 98.9796 | |
| gduggal-snapfb | SNP | * | HG002compoundhet | * | 83.3987 | 98.0094 | 72.5790 | 48.5976 | 25308 | 514 | 25579 | 9664 | 581 | 6.0120 | |
| rpoplin-dv42 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 88.9263 | 93.1683 | 85.0537 | 75.7901 | 3764 | 276 | 3642 | 640 | 581 | 90.7813 | |
| jlack-gatk | INDEL | D6_15 | * | * | 96.4774 | 96.4127 | 96.5422 | 54.8116 | 25156 | 936 | 25156 | 901 | 581 | 64.4839 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 64.4567 | 61.1138 | 68.1865 | 74.1910 | 1284 | 817 | 1316 | 614 | 580 | 94.4625 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 79.2227 | 71.1825 | 89.3103 | 43.3419 | 4918 | 1991 | 4921 | 589 | 580 | 98.4720 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 59.6174 | 68.6837 | 52.6656 | 65.6874 | 647 | 295 | 652 | 586 | 580 | 98.9761 | |
| gduggal-bwafb | INDEL | D6_15 | HG002compoundhet | homalt | 7.0180 | 95.8333 | 3.6424 | 68.7371 | 23 | 1 | 22 | 582 | 579 | 99.4845 | |
| ciseli-custom | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 95.3693 | 99.2326 | 91.7955 | 63.9797 | 20044 | 155 | 20005 | 1788 | 579 | 32.3826 | |
| ckim-gatk | INDEL | * | * | het | 99.4669 | 99.6616 | 99.2730 | 62.2737 | 193476 | 657 | 193095 | 1414 | 578 | 40.8769 | |
| gduggal-bwafb | INDEL | I1_5 | HG002compoundhet | homalt | 52.2901 | 97.8723 | 35.6751 | 79.4310 | 322 | 7 | 325 | 586 | 578 | 98.6348 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 95.5302 | 94.7711 | 96.3016 | 56.4893 | 16747 | 924 | 16743 | 643 | 577 | 89.7356 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 95.5302 | 94.7711 | 96.3016 | 56.4893 | 16747 | 924 | 16743 | 643 | 577 | 89.7356 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9460 | 98.5791 | 99.3156 | 73.7970 | 93107 | 1342 | 93014 | 641 | 576 | 89.8596 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 77.6919 | 72.9319 | 83.1165 | 45.6084 | 2689 | 998 | 2939 | 597 | 575 | 96.3149 | |
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.9458 | 97.7276 | 98.1651 | 56.3127 | 31265 | 727 | 31189 | 583 | 575 | 98.6278 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 69.4308 | 85.9873 | 58.2206 | 70.8929 | 810 | 132 | 818 | 587 | 575 | 97.9557 | |
| gduggal-snapplat | SNP | ti | map_l125_m2_e1 | het | 94.1854 | 93.9645 | 94.4074 | 84.4472 | 17935 | 1152 | 17961 | 1064 | 575 | 54.0414 | |
| jpowers-varprowl | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.8391 | 98.7777 | 96.9182 | 66.3842 | 54951 | 680 | 55130 | 1753 | 575 | 32.8009 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 78.4631 | 67.4647 | 93.7460 | 41.7311 | 3776 | 1821 | 8829 | 589 | 574 | 97.4533 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 94.3680 | 92.4804 | 96.3342 | 31.9134 | 16886 | 1373 | 16845 | 641 | 574 | 89.5476 | |
| mlin-fermikit | SNP | tv | map_l125_m0_e0 | * | 51.6639 | 38.2748 | 79.4606 | 60.5371 | 2538 | 4093 | 2534 | 655 | 574 | 87.6336 | |
| mlin-fermikit | SNP | tv | map_l125_m0_e0 | homalt | 55.7975 | 49.6173 | 63.7363 | 55.1608 | 1102 | 1119 | 1102 | 627 | 574 | 91.5470 | |
| ndellapenna-hhga | INDEL | D1_5 | HG002complexvar | * | 97.3122 | 96.7874 | 97.8426 | 54.8110 | 31664 | 1051 | 31656 | 698 | 573 | 82.0917 | |
| gduggal-snapplat | SNP | ti | map_l125_m2_e0 | het | 94.1306 | 93.9023 | 94.3600 | 84.4255 | 17725 | 1151 | 17751 | 1061 | 573 | 54.0057 | |
| gduggal-bwafb | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 82.5111 | 88.7732 | 77.0743 | 58.5831 | 1961 | 248 | 1960 | 583 | 573 | 98.2847 | |
| astatham-gatk | INDEL | * | * | het | 99.5127 | 99.4973 | 99.5281 | 60.7701 | 193157 | 976 | 192779 | 914 | 573 | 62.6915 | |
| gduggal-snapplat | INDEL | D1_5 | * | hetalt | 56.5026 | 42.2548 | 85.2469 | 84.6995 | 4329 | 5916 | 4403 | 762 | 572 | 75.0656 | |
| dgrover-gatk | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.2043 | 99.1106 | 99.2981 | 73.8671 | 93609 | 840 | 93517 | 661 | 572 | 86.5356 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 92.1861 | 94.9340 | 89.5928 | 65.6359 | 9201 | 491 | 9857 | 1145 | 571 | 49.8690 | |
| qzeng-custom | INDEL | I1_5 | HG002compoundhet | het | 92.1803 | 94.9412 | 89.5755 | 66.2595 | 807 | 43 | 5740 | 668 | 571 | 85.4790 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 24.2451 | 16.1226 | 48.8616 | 65.3414 | 563 | 2929 | 558 | 584 | 571 | 97.7740 | |
| gduggal-snapplat | SNP | ti | map_l125_m1_e0 | het | 93.9862 | 93.7479 | 94.2256 | 83.3757 | 17124 | 1142 | 17150 | 1051 | 571 | 54.3292 | |
| gduggal-snapfb | SNP | tv | * | het | 98.4503 | 99.7960 | 97.1404 | 29.1063 | 590497 | 1207 | 590839 | 17393 | 571 | 3.2829 | |