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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
40951-41000 / 86044 show all | |||||||||||||||
| gduggal-snapvard | INDEL | D16_PLUS | * | * | 10.7850 | 6.2058 | 41.1492 | 71.3717 | 421 | 6363 | 444 | 635 | 373 | 58.7402 | |
| ckim-dragen | SNP | ti | map_l100_m1_e0 | het | 98.1230 | 99.2485 | 97.0227 | 71.3768 | 29717 | 225 | 29720 | 912 | 87 | 9.5395 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 98.1559 | 97.0803 | 99.2556 | 71.3778 | 399 | 12 | 400 | 3 | 3 | 100.0000 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 34.8549 | 24.7113 | 59.1245 | 71.3782 | 963 | 2934 | 959 | 663 | 642 | 96.8326 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.8645 | 100.0000 | 97.7545 | 71.3796 | 653 | 0 | 653 | 15 | 14 | 93.3333 | |
| gduggal-snapfb | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 88.3624 | 85.5319 | 91.3867 | 71.3799 | 80784 | 13665 | 85516 | 8060 | 4292 | 53.2506 | |
| jpowers-varprowl | SNP | tv | map_l125_m1_e0 | homalt | 98.9113 | 98.4471 | 99.3798 | 71.3800 | 5769 | 91 | 5769 | 36 | 25 | 69.4444 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 96.5517 | 94.3820 | 98.8235 | 71.3805 | 84 | 5 | 84 | 1 | 0 | 0.0000 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.4570 | 99.2695 | 99.6453 | 71.3824 | 16851 | 124 | 16855 | 60 | 48 | 80.0000 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.4570 | 99.2695 | 99.6453 | 71.3824 | 16851 | 124 | 16855 | 60 | 48 | 80.0000 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.9799 | 98.8355 | 99.1247 | 71.3838 | 1358 | 16 | 1359 | 12 | 9 | 75.0000 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 84.4875 | 91.0761 | 78.7879 | 71.3873 | 694 | 68 | 702 | 189 | 31 | 16.4021 | |
| egarrison-hhga | INDEL | * | HG002compoundhet | * | 77.4600 | 76.5788 | 78.3617 | 71.3882 | 22943 | 7017 | 23485 | 6485 | 6131 | 94.5412 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.3348 | 98.9955 | 97.6830 | 71.3901 | 17640 | 179 | 17243 | 409 | 359 | 87.7751 | |
| dgrover-gatk | SNP | * | map_l100_m0_e0 | * | 99.2175 | 99.2266 | 99.2084 | 71.3904 | 32587 | 254 | 32583 | 260 | 57 | 21.9231 | |
| asubramanian-gatk | INDEL | I1_5 | HG002complexvar | hetalt | 97.2967 | 95.4229 | 99.2455 | 71.3930 | 1647 | 79 | 1710 | 13 | 11 | 84.6154 | |
| raldana-dualsentieon | SNP | * | map_l125_m2_e1 | * | 99.1573 | 99.2225 | 99.0922 | 71.3931 | 46835 | 367 | 46829 | 429 | 15 | 3.4965 | |
| ckim-vqsr | SNP | ti | map_siren | het | 91.0834 | 83.9713 | 99.5117 | 71.3937 | 52383 | 9999 | 52376 | 257 | 20 | 7.7821 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 98.1559 | 97.0803 | 99.2556 | 71.3982 | 399 | 12 | 400 | 3 | 3 | 100.0000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9345 | 98.2816 | 99.5962 | 71.4015 | 92826 | 1623 | 92734 | 376 | 307 | 81.6489 | |
| bgallagher-sentieon | SNP | tv | map_l100_m2_e0 | het | 99.1197 | 99.5817 | 98.6621 | 71.4019 | 15711 | 66 | 15707 | 213 | 25 | 11.7371 | |
| egarrison-hhga | SNP | * | map_l125_m2_e1 | het | 99.2353 | 98.7314 | 99.7444 | 71.4034 | 29264 | 376 | 29264 | 75 | 28 | 37.3333 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 94.8453 | 92.6241 | 97.1756 | 71.4036 | 1306 | 104 | 1273 | 37 | 32 | 86.4865 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 94.7598 | 91.0112 | 98.8304 | 71.4047 | 162 | 16 | 169 | 2 | 2 | 100.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.9808 | 97.2102 | 98.7638 | 71.4047 | 1568 | 45 | 1518 | 19 | 12 | 63.1579 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7085 | 99.7349 | 99.6820 | 71.4048 | 1881 | 5 | 1881 | 6 | 3 | 50.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | HG002compoundhet | homalt | 92.8474 | 93.6170 | 92.0904 | 71.4055 | 308 | 21 | 326 | 28 | 27 | 96.4286 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.2269 | 98.6744 | 99.7855 | 71.4089 | 1861 | 25 | 1861 | 4 | 2 | 50.0000 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 97.5982 | 96.9186 | 98.2874 | 71.4134 | 1321 | 42 | 1320 | 23 | 20 | 86.9565 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 92.8571 | 98.5656 | 87.7737 | 71.4137 | 481 | 7 | 481 | 67 | 61 | 91.0448 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.6199 | 97.4770 | 99.7898 | 71.4168 | 15184 | 393 | 15192 | 32 | 22 | 68.7500 | |
| hfeng-pmm3 | SNP | tv | map_l125_m2_e0 | * | 99.5176 | 99.4724 | 99.5629 | 71.4177 | 16402 | 87 | 16400 | 72 | 10 | 13.8889 | |
| gduggal-snapvard | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 79.4795 | 89.6706 | 71.3684 | 71.4189 | 43284 | 4986 | 93686 | 37585 | 31016 | 82.5223 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.4951 | 97.6558 | 99.3490 | 71.4213 | 4999 | 120 | 5036 | 33 | 7 | 21.2121 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 57.4031 | 85.2666 | 43.2650 | 71.4286 | 1551 | 268 | 1561 | 2047 | 2030 | 99.1695 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 57.4031 | 85.2666 | 43.2650 | 71.4286 | 1551 | 268 | 1561 | 2047 | 2030 | 99.1695 | |
| ltrigg-rtg2 | SNP | * | map_l150_m2_e0 | hetalt | 94.7368 | 90.0000 | 100.0000 | 71.4286 | 18 | 2 | 18 | 0 | 0 | ||
| ltrigg-rtg2 | SNP | * | map_l150_m2_e1 | hetalt | 94.7368 | 90.0000 | 100.0000 | 71.4286 | 18 | 2 | 18 | 0 | 0 | ||
| ltrigg-rtg1 | INDEL | D16_PLUS | map_l100_m2_e1 | hetalt | 86.7925 | 76.6667 | 100.0000 | 71.4286 | 23 | 7 | 20 | 0 | 0 | ||
| jmaeng-gatk | INDEL | I16_PLUS | tech_badpromoters | * | 100.0000 | 100.0000 | 100.0000 | 71.4286 | 4 | 0 | 4 | 0 | 0 | ||
| jmaeng-gatk | INDEL | I16_PLUS | tech_badpromoters | het | 100.0000 | 100.0000 | 100.0000 | 71.4286 | 2 | 0 | 2 | 0 | 0 | ||
| gduggal-snapplat | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 88.8889 | 80.0000 | 100.0000 | 71.4286 | 4 | 1 | 4 | 0 | 0 | ||
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 66.6667 | 100.0000 | 50.0000 | 71.4286 | 1 | 0 | 1 | 1 | 0 | 0.0000 | |
| gduggal-snapplat | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 88.8889 | 80.0000 | 100.0000 | 71.4286 | 4 | 1 | 4 | 0 | 0 | ||
| gduggal-snapvard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 0.0000 | 0.0000 | 50.0000 | 71.4286 | 0 | 61 | 1 | 1 | 1 | 100.0000 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 72.9446 | 66.2921 | 81.0811 | 71.4286 | 59 | 30 | 60 | 14 | 14 | 100.0000 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 37.5000 | 23.0769 | 100.0000 | 71.4286 | 3 | 10 | 2 | 0 | 0 | ||
| hfeng-pmm1 | INDEL | D16_PLUS | func_cds | * | 91.6667 | 91.6667 | 91.6667 | 71.4286 | 11 | 1 | 11 | 1 | 0 | 0.0000 | |
| egarrison-hhga | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 66.6667 | 100.0000 | 50.0000 | 71.4286 | 1 | 0 | 1 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | I16_PLUS | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 71.4286 | 2 | 0 | 2 | 0 | 0 | ||