PrecisionFDA
Truth Challenge
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Explore HG002 comparison results
Use this interactive explorer to filter all results across submission entries and multiple dimensions.
| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
34001-34050 / 86044 show all | |||||||||||||||
| qzeng-custom | INDEL | I6_15 | map_l125_m2_e0 | * | 66.8790 | 66.0377 | 67.7419 | 87.6000 | 35 | 18 | 84 | 40 | 3 | 7.5000 | |
| gduggal-snapvard | INDEL | C1_5 | map_l125_m0_e0 | * | 0.0000 | 0.0000 | 28.5714 | 96.1406 | 0 | 0 | 16 | 40 | 3 | 7.5000 | |
| gduggal-snapvard | INDEL | C1_5 | map_l125_m0_e0 | het | 0.0000 | 0.0000 | 20.0000 | 96.0254 | 0 | 0 | 10 | 40 | 3 | 7.5000 | |
| jmaeng-gatk | INDEL | D1_5 | map_l125_m0_e0 | * | 95.2178 | 98.1855 | 92.4242 | 92.0494 | 487 | 9 | 488 | 40 | 3 | 7.5000 | |
| jmaeng-gatk | SNP | * | map_l250_m0_e0 | * | 63.1215 | 46.9789 | 96.1649 | 98.1269 | 1003 | 1132 | 1003 | 40 | 3 | 7.5000 | |
| cchapple-custom | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 0.0000 | 0.0000 | 84.9624 | 96.2875 | 0 | 1 | 226 | 40 | 3 | 7.5000 | |
| cchapple-custom | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 0.0000 | 0.0000 | 84.9624 | 96.2875 | 0 | 1 | 226 | 40 | 3 | 7.5000 | |
| gduggal-snapvard | SNP | ti | map_l150_m2_e0 | het | 90.0316 | 96.5142 | 84.3650 | 84.9671 | 12432 | 449 | 12335 | 2286 | 171 | 7.4803 | |
| ghariani-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 95.7049 | 99.1018 | 92.5331 | 67.6378 | 1324 | 12 | 1326 | 107 | 8 | 7.4766 | |
| jlack-gatk | SNP | * | map_l100_m0_e0 | het | 93.8309 | 98.9295 | 89.2321 | 81.9092 | 20978 | 227 | 20974 | 2531 | 189 | 7.4674 | |
| ckim-gatk | INDEL | D1_5 | map_l150_m2_e0 | * | 95.0802 | 98.5583 | 91.8392 | 92.3713 | 752 | 11 | 754 | 67 | 5 | 7.4627 | |
| qzeng-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.2810 | 98.6274 | 95.9709 | 85.0094 | 14371 | 200 | 14363 | 603 | 45 | 7.4627 | |
| qzeng-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.2810 | 98.6274 | 95.9709 | 85.0094 | 14371 | 200 | 14363 | 603 | 45 | 7.4627 | |
| gduggal-snapvard | SNP | tv | map_l100_m2_e1 | * | 94.5392 | 97.0059 | 92.1948 | 76.2078 | 24526 | 757 | 24427 | 2068 | 154 | 7.4468 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 81.5043 | 75.5582 | 88.4663 | 84.8513 | 643 | 208 | 721 | 94 | 7 | 7.4468 | |
| eyeh-varpipe | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.2516 | 98.6776 | 88.3913 | 75.0612 | 4701 | 63 | 4500 | 591 | 44 | 7.4450 | |
| gduggal-bwaplat | SNP | ti | HG002compoundhet | het | 83.6361 | 90.0158 | 78.1008 | 46.8217 | 8556 | 949 | 8677 | 2433 | 181 | 7.4394 | |
| gduggal-snapvard | SNP | ti | map_l150_m1_e0 | het | 89.7218 | 96.4268 | 83.8886 | 83.9806 | 11928 | 442 | 11835 | 2273 | 169 | 7.4351 | |
| ckim-isaac | SNP | ti | * | het | 98.7325 | 97.5284 | 99.9667 | 15.6908 | 1250214 | 31683 | 1250525 | 417 | 31 | 7.4341 | |
| jlack-gatk | SNP | * | map_l150_m0_e0 | het | 91.7997 | 98.3753 | 86.0480 | 89.1426 | 7811 | 129 | 7808 | 1266 | 94 | 7.4250 | |
| gduggal-snapvard | SNP | * | map_l150_m2_e1 | * | 92.4051 | 96.3396 | 88.7794 | 82.5294 | 31031 | 1179 | 30628 | 3871 | 287 | 7.4141 | |
| hfeng-pmm2 | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.2862 | 98.9399 | 99.6350 | 37.4196 | 7373 | 79 | 7370 | 27 | 2 | 7.4074 | |
| hfeng-pmm3 | SNP | * | segdup | * | 99.7170 | 99.8183 | 99.6159 | 89.5042 | 28016 | 51 | 28010 | 108 | 8 | 7.4074 | |
| qzeng-custom | INDEL | D6_15 | map_l100_m1_e0 | homalt | 80.0602 | 87.5000 | 73.7864 | 75.5344 | 56 | 8 | 76 | 27 | 2 | 7.4074 | |
| qzeng-custom | SNP | * | func_cds | * | 99.7598 | 99.8182 | 99.7016 | 28.7413 | 18117 | 33 | 18040 | 54 | 4 | 7.4074 | |
| ltrigg-rtg2 | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3248 | 99.5674 | 99.0833 | 60.5130 | 17492 | 76 | 17510 | 162 | 12 | 7.4074 | |
| ltrigg-rtg2 | SNP | tv | map_l100_m0_e0 | * | 98.6223 | 97.5189 | 99.7508 | 54.0500 | 10809 | 275 | 10808 | 27 | 2 | 7.4074 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 76.5217 | 100.0000 | 61.9718 | 67.8733 | 45 | 0 | 44 | 27 | 2 | 7.4074 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.0423 | 98.7194 | 99.3672 | 50.0468 | 4240 | 55 | 4240 | 27 | 2 | 7.4074 | |
| bgallagher-sentieon | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.6756 | 99.9350 | 99.4176 | 34.7502 | 4613 | 3 | 4609 | 27 | 2 | 7.4074 | |
| bgallagher-sentieon | SNP | tv | map_l250_m0_e0 | het | 96.6350 | 97.9021 | 95.4003 | 93.3341 | 560 | 12 | 560 | 27 | 2 | 7.4074 | |
| cchapple-custom | INDEL | * | map_l250_m2_e0 | het | 91.3070 | 94.2857 | 88.5106 | 96.0027 | 198 | 12 | 208 | 27 | 2 | 7.4074 | |
| cchapple-custom | INDEL | * | map_l250_m2_e1 | het | 91.3456 | 94.3128 | 88.5593 | 96.0927 | 199 | 12 | 209 | 27 | 2 | 7.4074 | |
| eyeh-varpipe | SNP | tv | map_l250_m0_e0 | het | 97.3196 | 99.3007 | 95.4160 | 94.4664 | 568 | 4 | 562 | 27 | 2 | 7.4074 | |
| ckim-vqsr | INDEL | * | map_l250_m1_e0 | * | 93.0757 | 94.7541 | 91.4557 | 97.2688 | 289 | 16 | 289 | 27 | 2 | 7.4074 | |
| ckim-vqsr | INDEL | * | map_l250_m2_e0 | * | 93.4524 | 94.8640 | 92.0821 | 97.4260 | 314 | 17 | 314 | 27 | 2 | 7.4074 | |
| ckim-vqsr | INDEL | * | map_l250_m2_e1 | * | 93.4911 | 94.8949 | 92.1283 | 97.4798 | 316 | 17 | 316 | 27 | 2 | 7.4074 | |
| ckim-vqsr | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.5068 | 99.4678 | 99.5459 | 59.1769 | 17756 | 95 | 17755 | 81 | 6 | 7.4074 | |
| ckim-gatk | INDEL | * | map_l150_m0_e0 | * | 94.2458 | 98.4436 | 90.3915 | 94.6603 | 506 | 8 | 508 | 54 | 4 | 7.4074 | |
| ckim-dragen | INDEL | D1_5 | map_l150_m2_e1 | het | 96.2144 | 97.5096 | 94.9533 | 90.7487 | 509 | 13 | 508 | 27 | 2 | 7.4074 | |
| ckim-dragen | SNP | tv | map_l150_m0_e0 | het | 97.0162 | 97.7840 | 96.2604 | 84.6993 | 2780 | 63 | 2780 | 108 | 8 | 7.4074 | |
| cchapple-custom | INDEL | C1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 0.0000 | 0.0000 | 74.7664 | 96.5316 | 0 | 0 | 80 | 27 | 2 | 7.4074 | |
| cchapple-custom | INDEL | D1_5 | map_l125_m2_e0 | het | 95.2845 | 97.3822 | 93.2752 | 86.3249 | 744 | 20 | 749 | 54 | 4 | 7.4074 | |
| cchapple-custom | INDEL | D1_5 | map_l125_m2_e1 | het | 95.3203 | 97.4026 | 93.3251 | 86.4330 | 750 | 20 | 755 | 54 | 4 | 7.4074 | |
| cchapple-custom | SNP | tv | * | het | 99.6701 | 99.8702 | 99.4708 | 26.9512 | 590928 | 768 | 591553 | 3147 | 233 | 7.4039 | |
| hfeng-pmm1 | SNP | ti | * | het | 99.9312 | 99.8931 | 99.9694 | 16.7684 | 1280521 | 1370 | 1280470 | 392 | 29 | 7.3980 | |
| jlack-gatk | SNP | * | map_l250_m2_e0 | * | 93.5078 | 97.9074 | 89.4865 | 92.8768 | 7720 | 165 | 7720 | 907 | 67 | 7.3870 | |
| qzeng-custom | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 97.6562 | 98.9840 | 96.3636 | 77.0001 | 3215 | 33 | 3233 | 122 | 9 | 7.3771 | |
| ckim-gatk | SNP | * | map_l100_m1_e0 | het | 92.2588 | 87.5769 | 97.4696 | 81.5171 | 39724 | 5635 | 39713 | 1031 | 76 | 7.3715 | |
| gduggal-snapvard | SNP | * | map_l150_m2_e0 | * | 92.3600 | 96.3299 | 88.7044 | 82.4713 | 30683 | 1169 | 30289 | 3857 | 284 | 7.3632 | |