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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
60701-60750 / 86044 show all | |||||||||||||||
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.2737 | 91.9271 | 98.8732 | 77.2144 | 353 | 31 | 351 | 4 | 2 | 50.0000 | |
| ckim-vqsr | SNP | ti | map_l100_m0_e0 | het | 80.8690 | 68.4116 | 98.8733 | 87.2610 | 9566 | 4417 | 9565 | 109 | 1 | 0.9174 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.1110 | 97.3601 | 98.8735 | 45.3846 | 35626 | 966 | 45291 | 516 | 450 | 87.2093 | |
| gduggal-bwaplat | SNP | tv | segdup | het | 98.3560 | 97.8438 | 98.8736 | 96.0991 | 5173 | 114 | 5179 | 59 | 6 | 10.1695 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 91.7942 | 85.6604 | 98.8743 | 47.1754 | 454 | 76 | 527 | 6 | 6 | 100.0000 | |
| cchapple-custom | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2564 | 99.6414 | 98.8744 | 60.9154 | 35292 | 127 | 35487 | 404 | 50 | 12.3762 | |
| bgallagher-sentieon | SNP | * | map_l150_m1_e0 | * | 99.1019 | 99.3303 | 98.8746 | 75.7599 | 30404 | 205 | 30398 | 346 | 61 | 17.6301 | |
| rpoplin-dv42 | SNP | ti | map_l250_m2_e0 | * | 98.5577 | 98.2428 | 98.8746 | 88.2672 | 4920 | 88 | 4920 | 56 | 37 | 66.0714 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 75.1664 | 60.6286 | 98.8753 | 39.2261 | 5633 | 3658 | 5187 | 59 | 47 | 79.6610 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 75.1664 | 60.6286 | 98.8753 | 39.2261 | 5633 | 3658 | 5187 | 59 | 47 | 79.6610 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 98.1764 | 97.4871 | 98.8756 | 71.7313 | 1319 | 34 | 1319 | 15 | 8 | 53.3333 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.6420 | 98.4090 | 98.8761 | 66.2789 | 19546 | 316 | 20235 | 230 | 48 | 20.8696 | |
| gduggal-bwafb | INDEL | I1_5 | HG002complexvar | * | 97.5502 | 96.2593 | 98.8762 | 54.2720 | 32115 | 1248 | 32201 | 366 | 326 | 89.0710 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | het | 82.5379 | 70.8333 | 98.8764 | 33.5821 | 17 | 7 | 88 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.0619 | 99.2481 | 98.8764 | 82.8296 | 264 | 2 | 264 | 3 | 1 | 33.3333 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 96.2535 | 93.7662 | 98.8764 | 76.3769 | 361 | 24 | 352 | 4 | 3 | 75.0000 | |
| hfeng-pmm2 | INDEL | D6_15 | segdup | het | 97.2376 | 95.6522 | 98.8764 | 94.8044 | 88 | 4 | 88 | 1 | 0 | 0.0000 | |
| jli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.8764 | 98.8764 | 98.8764 | 69.7279 | 88 | 1 | 88 | 1 | 0 | 0.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.3114 | 97.7528 | 98.8764 | 76.5789 | 87 | 2 | 88 | 1 | 0 | 0.0000 | |
| dgrover-gatk | SNP | * | map_l125_m0_e0 | * | 98.9327 | 98.9889 | 98.8765 | 77.4655 | 19189 | 196 | 19186 | 218 | 48 | 22.0183 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.8086 | 94.8250 | 98.8768 | 51.0057 | 2547 | 139 | 2553 | 29 | 2 | 6.8966 | |
| raldana-dualsentieon | SNP | ti | map_l150_m2_e1 | * | 98.9365 | 98.9963 | 98.8768 | 75.5106 | 20515 | 208 | 20511 | 233 | 9 | 3.8627 | |
| hfeng-pmm1 | INDEL | D6_15 | * | het | 98.2571 | 97.6449 | 98.8769 | 58.2726 | 11319 | 273 | 11269 | 128 | 111 | 86.7188 | |
| qzeng-custom | SNP | * | HG002compoundhet | homalt | 98.8868 | 98.8963 | 98.8772 | 42.3069 | 10663 | 119 | 8190 | 93 | 74 | 79.5699 | |
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.0168 | 97.1706 | 98.8778 | 83.5902 | 2301 | 67 | 2379 | 27 | 22 | 81.4815 | |
| bgallagher-sentieon | SNP | tv | map_l125_m2_e1 | * | 99.1800 | 99.4837 | 98.8781 | 73.5318 | 16571 | 86 | 16569 | 188 | 28 | 14.8936 | |
| egarrison-hhga | INDEL | I1_5 | map_l100_m1_e0 | * | 98.8042 | 98.7304 | 98.8781 | 83.3892 | 1322 | 17 | 1322 | 15 | 3 | 20.0000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.3350 | 95.8393 | 98.8782 | 52.0725 | 36325 | 1577 | 36139 | 410 | 384 | 93.6585 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.1574 | 95.4955 | 98.8782 | 87.2783 | 636 | 30 | 617 | 7 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.1574 | 95.4955 | 98.8782 | 87.2783 | 636 | 30 | 617 | 7 | 0 | 0.0000 | |
| asubramanian-gatk | SNP | * | HG002compoundhet | * | 97.7516 | 96.6501 | 98.8785 | 41.8929 | 24957 | 865 | 24950 | 283 | 28 | 9.8940 | |
| cchapple-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.1128 | 99.3482 | 98.8786 | 72.9414 | 30940 | 203 | 30949 | 351 | 41 | 11.6809 | |
| cchapple-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.1128 | 99.3482 | 98.8786 | 72.9414 | 30940 | 203 | 30949 | 351 | 41 | 11.6809 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.1754 | 99.4737 | 98.8789 | 38.7923 | 1323 | 7 | 1323 | 15 | 13 | 86.6667 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.1004 | 99.3228 | 98.8789 | 34.2183 | 440 | 3 | 441 | 5 | 5 | 100.0000 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.2126 | 99.5485 | 98.8789 | 32.5265 | 441 | 2 | 441 | 5 | 4 | 80.0000 | |
| gduggal-bwaplat | INDEL | * | map_l100_m2_e1 | * | 80.6558 | 68.1044 | 98.8790 | 92.5655 | 2558 | 1198 | 2558 | 29 | 11 | 37.9310 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.7268 | 94.6662 | 98.8792 | 50.6141 | 2822 | 159 | 2823 | 32 | 28 | 87.5000 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.2950 | 93.8423 | 98.8793 | 50.2372 | 7879 | 517 | 13588 | 154 | 79 | 51.2987 | |
| hfeng-pmm3 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 93.6340 | 88.9169 | 98.8796 | 87.9595 | 706 | 88 | 706 | 8 | 3 | 37.5000 | |
| jlack-gatk | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.3650 | 99.8551 | 98.8796 | 40.1582 | 3445 | 5 | 3442 | 39 | 2 | 5.1282 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.0761 | 97.2854 | 98.8798 | 74.4855 | 1326 | 37 | 1324 | 15 | 8 | 53.3333 | |
| egarrison-hhga | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 98.5362 | 98.1948 | 98.8800 | 67.3655 | 4678 | 86 | 4679 | 53 | 21 | 39.6226 | |
| ckim-vqsr | SNP | * | map_l125_m1_e0 | * | 69.8181 | 53.9590 | 98.8800 | 88.0425 | 24458 | 20869 | 24455 | 277 | 5 | 1.8051 | |
| hfeng-pmm3 | INDEL | D1_5 | map_l125_m2_e1 | * | 98.9647 | 99.0493 | 98.8803 | 84.7056 | 1146 | 11 | 1148 | 13 | 3 | 23.0769 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.0654 | 99.2509 | 98.8806 | 66.5000 | 265 | 2 | 265 | 3 | 3 | 100.0000 | |
| ltrigg-rtg1 | INDEL | C1_5 | * | hetalt | 99.4371 | 100.0000 | 98.8806 | 95.8674 | 1 | 0 | 265 | 3 | 3 | 100.0000 | |
| gduggal-bwafb | INDEL | I1_5 | map_l100_m2_e0 | homalt | 99.3440 | 99.8117 | 98.8806 | 82.8095 | 530 | 1 | 530 | 6 | 4 | 66.6667 | |
| gduggal-bwaplat | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 85.3755 | 75.1159 | 98.8810 | 48.3447 | 972 | 322 | 972 | 11 | 10 | 90.9091 | |
| jlack-gatk | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.4304 | 97.9839 | 98.8810 | 71.7122 | 972 | 20 | 972 | 11 | 2 | 18.1818 | |