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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
12301-12350 / 86044 show all | |||||||||||||||
| qzeng-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 90.2393 | 98.2456 | 83.4395 | 66.8543 | 392 | 7 | 393 | 78 | 39 | 50.0000 | |
| ndellapenna-hhga | SNP | ti | map_l100_m2_e0 | * | 99.3576 | 98.8807 | 99.8392 | 63.3838 | 48413 | 548 | 48415 | 78 | 40 | 51.2821 | |
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 22.1517 | 13.2826 | 66.6667 | 82.1918 | 157 | 1025 | 156 | 78 | 60 | 76.9231 | |
| gduggal-snapfb | SNP | tv | lowcmp_SimpleRepeat_triTR_51to200 | * | 2.5000 | 100.0000 | 1.2658 | 65.6522 | 1 | 0 | 1 | 78 | 1 | 1.2821 | |
| gduggal-snapplat | INDEL | * | map_l125_m0_e0 | het | 79.4200 | 74.1056 | 85.5556 | 95.1768 | 435 | 152 | 462 | 78 | 12 | 15.3846 | |
| hfeng-pmm1 | INDEL | * | HG002complexvar | het | 98.8731 | 97.9378 | 99.8265 | 56.4583 | 45259 | 953 | 44888 | 78 | 43 | 55.1282 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 43.9926 | 38.2022 | 51.8519 | 68.8462 | 68 | 110 | 84 | 78 | 56 | 71.7949 | |
| gduggal-snapvard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 58.8919 | 70.3704 | 50.6329 | 68.7129 | 57 | 24 | 80 | 78 | 56 | 71.7949 | |
| gduggal-snapvard | INDEL | C6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 0.0000 | 0.0000 | 31.5789 | 81.2500 | 0 | 0 | 36 | 78 | 13 | 16.6667 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 68.7985 | 52.6643 | 99.1844 | 57.0543 | 9567 | 8599 | 9486 | 78 | 41 | 52.5641 | |
| gduggal-bwafb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.0773 | 99.6780 | 96.5272 | 70.4668 | 2167 | 7 | 2168 | 78 | 5 | 6.4103 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 53.6602 | 38.0295 | 91.1060 | 74.8783 | 799 | 1302 | 799 | 78 | 48 | 61.5385 | |
| gduggal-bwavard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 97.0619 | 97.7461 | 96.3872 | 69.9220 | 2125 | 49 | 2081 | 78 | 11 | 14.1026 | |
| eyeh-varpipe | INDEL | C6_15 | * | * | 89.4022 | 100.0000 | 80.8354 | 93.6057 | 7 | 0 | 329 | 78 | 51 | 65.3846 | |
| eyeh-varpipe | INDEL | I1_5 | map_l100_m2_e0 | * | 96.3034 | 96.1257 | 96.4817 | 82.0384 | 1315 | 53 | 2139 | 78 | 60 | 76.9231 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 86.4064 | 90.9774 | 82.2727 | 51.2195 | 363 | 36 | 362 | 78 | 78 | 100.0000 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.0280 | 94.8346 | 99.3253 | 40.5686 | 6334 | 345 | 11482 | 78 | 47 | 60.2564 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 89.9308 | 89.1078 | 90.7692 | 60.4401 | 769 | 94 | 767 | 78 | 76 | 97.4359 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 68.7985 | 52.6643 | 99.1844 | 57.0543 | 9567 | 8599 | 9486 | 78 | 41 | 52.5641 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.0004 | 93.1933 | 98.9817 | 26.3036 | 7544 | 551 | 7582 | 78 | 72 | 92.3077 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 94.5362 | 98.9362 | 90.5109 | 61.6962 | 744 | 8 | 744 | 78 | 78 | 100.0000 | |
| anovak-vg | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 98.4369 | 98.7908 | 98.0854 | 58.8485 | 3840 | 47 | 3996 | 78 | 33 | 42.3077 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 71.6605 | 91.8919 | 58.7302 | 73.5664 | 136 | 12 | 111 | 78 | 77 | 98.7179 | |
| bgallagher-sentieon | SNP | ti | map_l250_m1_e0 | het | 98.1612 | 98.9218 | 97.4121 | 90.4001 | 2936 | 32 | 2936 | 78 | 16 | 20.5128 | |
| astatham-gatk | INDEL | D1_5 | HG002complexvar | * | 99.5714 | 99.3825 | 99.7611 | 58.5986 | 32513 | 202 | 32567 | 78 | 66 | 84.6154 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 93.6669 | 99.5017 | 88.4786 | 52.4912 | 599 | 3 | 599 | 78 | 77 | 98.7179 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1951 | 98.6340 | 99.7626 | 72.6726 | 32782 | 454 | 32775 | 78 | 58 | 74.3590 | |
| hfeng-pmm3 | SNP | tv | map_l100_m2_e0 | * | 99.6443 | 99.6005 | 99.6881 | 66.3015 | 24933 | 100 | 24929 | 78 | 10 | 12.8205 | |
| jli-custom | INDEL | * | * | hetalt | 96.4996 | 93.5214 | 99.6737 | 57.4952 | 23602 | 1635 | 23825 | 78 | 76 | 97.4359 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 88.7128 | 96.9359 | 81.7757 | 44.7028 | 348 | 11 | 350 | 78 | 77 | 98.7179 | |
| hfeng-pmm2 | SNP | ti | map_l250_m2_e1 | * | 98.8122 | 99.1529 | 98.4739 | 90.0047 | 5033 | 43 | 5033 | 78 | 9 | 11.5385 | |
| dgrover-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.5866 | 99.8975 | 99.2777 | 41.4403 | 10721 | 11 | 10721 | 78 | 1 | 1.2821 | |
| dgrover-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.3508 | 99.8517 | 98.8550 | 44.7482 | 6734 | 10 | 6734 | 78 | 1 | 1.2821 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.7434 | 96.7060 | 96.7809 | 72.0820 | 2378 | 81 | 2345 | 78 | 34 | 43.5897 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.3777 | 93.7799 | 97.0308 | 84.5325 | 2548 | 169 | 2549 | 78 | 41 | 52.5641 | |
| raldana-dualsentieon | SNP | ti | HG002complexvar | * | 99.8917 | 99.7990 | 99.9846 | 17.3582 | 507414 | 1022 | 507354 | 78 | 29 | 37.1795 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 88.8647 | 90.8347 | 86.9783 | 67.1961 | 555 | 56 | 521 | 78 | 77 | 98.7179 | |
| raldana-dualsentieon | INDEL | I16_PLUS | * | homalt | 97.4343 | 99.7438 | 95.2294 | 67.8023 | 1557 | 4 | 1557 | 78 | 76 | 97.4359 | |
| jpowers-varprowl | INDEL | I16_PLUS | HG002compoundhet | homalt | 7.1429 | 100.0000 | 3.7037 | 66.6667 | 3 | 0 | 3 | 78 | 77 | 98.7179 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 75.2854 | 64.8571 | 89.7098 | 61.7172 | 681 | 369 | 680 | 78 | 71 | 91.0256 | |
| jpowers-varprowl | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.3232 | 99.9179 | 98.7356 | 57.1091 | 6083 | 5 | 6091 | 78 | 58 | 74.3590 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 89.2190 | 94.9425 | 84.1463 | 67.3090 | 413 | 22 | 414 | 78 | 75 | 96.1538 | |
| jli-custom | SNP | * | map_l150_m0_e0 | * | 98.7204 | 98.1051 | 99.3435 | 75.0933 | 11804 | 228 | 11804 | 78 | 29 | 37.1795 | |
| jli-custom | SNP | tv | HG002complexvar | * | 99.9252 | 99.8822 | 99.9683 | 21.9781 | 245862 | 290 | 245791 | 78 | 33 | 42.3077 | |
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 93.9195 | 98.7443 | 89.5442 | 81.8359 | 865 | 11 | 668 | 78 | 76 | 97.4359 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.8981 | 99.9175 | 97.8993 | 62.0929 | 3635 | 3 | 3635 | 78 | 75 | 96.1538 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 98.0184 | 98.3990 | 97.6407 | 68.5083 | 3196 | 52 | 3228 | 78 | 3 | 3.8462 | |
| ltrigg-rtg1 | SNP | ti | map_l100_m2_e0 | het | 99.0198 | 98.3084 | 99.7416 | 57.0120 | 30104 | 518 | 30106 | 78 | 7 | 8.9744 | |
| jli-custom | INDEL | D6_15 | * | homalt | 99.2923 | 99.8103 | 98.7797 | 52.7778 | 6314 | 12 | 6314 | 78 | 76 | 97.4359 | |
| jli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.8687 | 99.7876 | 97.9666 | 56.5178 | 3758 | 8 | 3758 | 78 | 76 | 97.4359 | |