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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
59151-59200 / 86044 show all | |||||||||||||||
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 95.5521 | 92.6829 | 98.6047 | 87.0091 | 228 | 18 | 212 | 3 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l100_m2_e0 | * | 98.9747 | 98.6842 | 99.2669 | 82.6860 | 1350 | 18 | 1354 | 10 | 3 | 30.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l100_m2_e1 | * | 98.9946 | 98.7097 | 99.2811 | 82.7868 | 1377 | 18 | 1381 | 10 | 3 | 30.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_siren | het | 99.2252 | 98.9292 | 99.5230 | 79.8146 | 1663 | 18 | 1669 | 8 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.1339 | 92.7126 | 97.6852 | 79.5455 | 229 | 18 | 211 | 5 | 3 | 60.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 94.6479 | 90.3226 | 99.4083 | 69.9288 | 168 | 18 | 168 | 1 | 1 | 100.0000 | |
| hfeng-pmm3 | SNP | tv | map_l100_m1_e0 | homalt | 99.8285 | 99.8010 | 99.8562 | 62.3809 | 9025 | 18 | 9025 | 13 | 5 | 38.4615 | |
| hfeng-pmm3 | SNP | tv | map_l100_m2_e0 | homalt | 99.8317 | 99.8046 | 99.8588 | 64.7570 | 9196 | 18 | 9196 | 13 | 5 | 38.4615 | |
| hfeng-pmm3 | SNP | tv | map_l100_m2_e1 | homalt | 99.8333 | 99.8065 | 99.8602 | 64.7574 | 9284 | 18 | 9284 | 13 | 5 | 38.4615 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9017 | 99.8231 | 99.9803 | 53.8406 | 10160 | 18 | 10160 | 2 | 2 | 100.0000 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.3905 | 98.9595 | 99.8252 | 33.0994 | 1712 | 18 | 1713 | 3 | 2 | 66.6667 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.4177 | 93.7063 | 99.2908 | 56.4815 | 268 | 18 | 280 | 2 | 2 | 100.0000 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 96.3542 | 95.3608 | 97.3684 | 75.3407 | 370 | 18 | 370 | 10 | 7 | 70.0000 | |
| jlack-gatk | INDEL | I1_5 | HG002compoundhet | het | 90.5365 | 97.8824 | 84.2162 | 85.4468 | 832 | 18 | 779 | 146 | 134 | 91.7808 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 93.9898 | 93.7500 | 94.2308 | 79.6557 | 270 | 18 | 245 | 15 | 9 | 60.0000 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.3939 | 98.9796 | 97.8151 | 89.1397 | 1746 | 18 | 1746 | 39 | 21 | 53.8462 | |
| jlack-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.8871 | 98.1073 | 99.6795 | 84.5007 | 933 | 18 | 933 | 3 | 3 | 100.0000 | |
| jlack-gatk | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.6954 | 99.4790 | 99.9128 | 62.0351 | 3437 | 18 | 3437 | 3 | 3 | 100.0000 | |
| jlack-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.3078 | 99.3917 | 99.2240 | 48.4791 | 2941 | 18 | 2941 | 23 | 2 | 8.6957 | |
| jlack-gatk | SNP | tv | map_l250_m1_e0 | homalt | 98.5303 | 97.8972 | 99.1716 | 86.3357 | 838 | 18 | 838 | 7 | 5 | 71.4286 | |
| jlack-gatk | SNP | tv | map_l250_m2_e0 | homalt | 98.6581 | 98.0790 | 99.2441 | 87.2434 | 919 | 18 | 919 | 7 | 5 | 71.4286 | |
| jlack-gatk | SNP | tv | map_l250_m2_e1 | homalt | 98.6709 | 98.0973 | 99.2513 | 87.3083 | 928 | 18 | 928 | 7 | 5 | 71.4286 | |
| jlack-gatk | SNP | tv | segdup | * | 97.7319 | 99.7890 | 95.7578 | 94.5195 | 8514 | 18 | 8510 | 377 | 7 | 1.8568 | |
| jli-custom | INDEL | * | map_l150_m2_e0 | het | 98.1776 | 98.0132 | 98.3425 | 89.4239 | 888 | 18 | 890 | 15 | 4 | 26.6667 | |
| hfeng-pmm2 | SNP | ti | map_l100_m0_e0 | homalt | 99.7813 | 99.7685 | 99.7941 | 63.0398 | 7756 | 18 | 7756 | 16 | 7 | 43.7500 | |
| hfeng-pmm2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.2470 | 98.6527 | 99.8485 | 51.0567 | 1318 | 18 | 1318 | 2 | 0 | 0.0000 | |
| hfeng-pmm2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.8194 | 97.8947 | 99.7616 | 48.6536 | 837 | 18 | 837 | 2 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | * | map_l100_m0_e0 | het | 98.1428 | 98.2370 | 98.0488 | 85.0974 | 1003 | 18 | 1005 | 20 | 2 | 10.0000 | |
| hfeng-pmm3 | INDEL | * | map_l150_m2_e0 | het | 97.9638 | 98.0132 | 97.9144 | 88.9709 | 888 | 18 | 892 | 19 | 3 | 15.7895 | |
| ciseli-custom | INDEL | D16_PLUS | map_l100_m0_e0 | * | 48.0349 | 35.7143 | 73.3333 | 93.9271 | 10 | 18 | 11 | 4 | 1 | 25.0000 | |
| ciseli-custom | INDEL | D6_15 | map_l125_m1_e0 | hetalt | 0.0000 | 5.2632 | 0.0000 | 0.0000 | 1 | 18 | 0 | 0 | 0 | ||
| ciseli-custom | INDEL | D6_15 | map_l125_m2_e0 | hetalt | 0.0000 | 5.2632 | 0.0000 | 0.0000 | 1 | 18 | 0 | 0 | 0 | ||
| ciseli-custom | INDEL | D6_15 | segdup | het | 78.3734 | 80.4348 | 76.4151 | 94.8494 | 74 | 18 | 81 | 25 | 8 | 32.0000 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 18 | 0 | 0 | 0 | |||
| ciseli-custom | INDEL | I16_PLUS | map_l100_m1_e0 | het | 0.0000 | 0.0000 | 98.7805 | 0 | 18 | 0 | 1 | 0 | 0.0000 | ||
| ciseli-custom | INDEL | I16_PLUS | map_l100_m2_e0 | het | 0.0000 | 0.0000 | 98.9899 | 0 | 18 | 0 | 1 | 0 | 0.0000 | ||
| ciseli-custom | INDEL | I16_PLUS | map_l100_m2_e1 | het | 0.0000 | 0.0000 | 99.0196 | 0 | 18 | 0 | 1 | 0 | 0.0000 | ||
| ciseli-custom | INDEL | I16_PLUS | map_siren | homalt | 19.3548 | 14.2857 | 30.0000 | 87.1795 | 3 | 18 | 3 | 7 | 4 | 57.1429 | |
| ciseli-custom | INDEL | I1_5 | map_l125_m2_e0 | hetalt | 0.0000 | 5.2632 | 0.0000 | 0.0000 | 1 | 18 | 0 | 0 | 0 | ||
| ciseli-custom | INDEL | I1_5 | map_l125_m2_e1 | hetalt | 0.0000 | 5.2632 | 0.0000 | 0.0000 | 1 | 18 | 0 | 0 | 0 | ||
| ckim-dragen | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.7905 | 98.1855 | 99.4030 | 70.9117 | 974 | 18 | 999 | 6 | 2 | 33.3333 | |
| ckim-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.5308 | 99.1852 | 92.1362 | 66.1398 | 2191 | 18 | 2191 | 187 | 184 | 98.3957 | |
| ckim-gatk | INDEL | * | map_l100_m2_e1 | hetalt | 92.6829 | 86.3636 | 100.0000 | 87.5536 | 114 | 18 | 116 | 0 | 0 | ||
| ckim-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 96.7378 | 94.8571 | 98.6945 | 34.1924 | 332 | 18 | 378 | 5 | 5 | 100.0000 | |
| cchapple-custom | INDEL | I1_5 | map_l100_m0_e0 | * | 96.5832 | 96.6851 | 96.4815 | 84.1223 | 525 | 18 | 521 | 19 | 5 | 26.3158 | |
| cchapple-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.8722 | 97.8873 | 99.8771 | 70.5393 | 834 | 18 | 813 | 1 | 1 | 100.0000 | |
| cchapple-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.6262 | 99.2553 | 100.0000 | 69.5205 | 2399 | 18 | 2371 | 0 | 0 | ||
| cchapple-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 91.6233 | 89.0909 | 94.3038 | 89.1185 | 147 | 18 | 149 | 9 | 0 | 0.0000 | |
| cchapple-custom | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.3439 | 99.7585 | 96.9689 | 38.4203 | 7434 | 18 | 7454 | 233 | 3 | 1.2876 | |
| ckim-dragen | INDEL | D6_15 | HG002compoundhet | het | 95.5765 | 97.8972 | 93.3633 | 64.0953 | 838 | 18 | 830 | 59 | 57 | 96.6102 | |