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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
5501-5550 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.9301 | 95.6489 | 98.2460 | 63.4208 | 13981 | 636 | 13611 | 243 | 222 | 91.3580 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.1235 | 99.2295 | 99.0178 | 67.7817 | 13651 | 106 | 13609 | 135 | 117 | 86.6667 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.1235 | 99.2295 | 99.0178 | 67.7817 | 13651 | 106 | 13609 | 135 | 117 | 86.6667 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.9199 | 95.6831 | 98.1890 | 62.4288 | 13986 | 631 | 13609 | 251 | 218 | 86.8526 | |
| gduggal-bwaplat | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 86.4957 | 77.2826 | 98.2029 | 77.4578 | 13577 | 3991 | 13607 | 249 | 50 | 20.0803 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.0981 | 99.2004 | 98.9959 | 68.2271 | 13647 | 110 | 13606 | 138 | 117 | 84.7826 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0981 | 99.2004 | 98.9959 | 68.2271 | 13647 | 110 | 13606 | 138 | 117 | 84.7826 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.0727 | 99.1931 | 98.9527 | 67.4865 | 13646 | 111 | 13605 | 144 | 128 | 88.8889 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0727 | 99.1931 | 98.9527 | 67.4865 | 13646 | 111 | 13605 | 144 | 128 | 88.8889 | |
| ltrigg-rtg1 | SNP | ti | map_l100_m0_e0 | het | 98.4715 | 97.2109 | 99.7652 | 55.6290 | 13593 | 390 | 13597 | 32 | 4 | 12.5000 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.2696 | 97.9874 | 96.5623 | 64.0273 | 12269 | 252 | 13595 | 484 | 266 | 54.9587 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.9182 | 95.5942 | 98.2795 | 62.6246 | 13973 | 644 | 13595 | 238 | 216 | 90.7563 | |
| anovak-vg | SNP | * | map_l125_m1_e0 | homalt | 89.5021 | 81.4552 | 99.3132 | 65.1171 | 13770 | 3135 | 13593 | 94 | 78 | 82.9787 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.0685 | 99.1132 | 99.0238 | 69.1438 | 13635 | 122 | 13593 | 134 | 112 | 83.5821 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.0685 | 99.1132 | 99.0238 | 69.1438 | 13635 | 122 | 13593 | 134 | 112 | 83.5821 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.8086 | 98.8224 | 96.8153 | 66.1962 | 13595 | 162 | 13589 | 447 | 406 | 90.8277 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.8086 | 98.8224 | 96.8153 | 66.1962 | 13595 | 162 | 13589 | 447 | 406 | 90.8277 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 89.4795 | 84.4436 | 95.1541 | 60.5296 | 13576 | 2501 | 13588 | 692 | 434 | 62.7168 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 89.4795 | 84.4436 | 95.1541 | 60.5296 | 13576 | 2501 | 13588 | 692 | 434 | 62.7168 | |
| 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 | |
| gduggal-snapplat | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 83.4678 | 77.0663 | 91.0292 | 80.6522 | 13539 | 4029 | 13577 | 1338 | 103 | 7.6981 | |
| raldana-dualsentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.2627 | 95.4437 | 97.0959 | 63.8638 | 13951 | 666 | 13574 | 406 | 386 | 95.0739 | |
| ciseli-custom | SNP | * | map_l150_m2_e0 | het | 73.2869 | 67.4862 | 80.1784 | 84.7273 | 13587 | 6546 | 13571 | 3355 | 112 | 3.3383 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.2085 | 99.0041 | 99.4137 | 68.4982 | 13620 | 137 | 13565 | 80 | 52 | 65.0000 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.2085 | 99.0041 | 99.4137 | 68.4982 | 13620 | 137 | 13565 | 80 | 52 | 65.0000 | |
| cchapple-custom | SNP | ti | map_l100_m0_e0 | het | 96.2084 | 96.8676 | 95.5581 | 74.9532 | 13545 | 438 | 13553 | 630 | 172 | 27.3016 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 58.8469 | 92.5566 | 43.1364 | 52.0545 | 13529 | 1088 | 13550 | 17862 | 17494 | 97.9398 | |
| gduggal-snapfb | SNP | ti | map_l100_m0_e0 | het | 96.0596 | 96.8390 | 95.2927 | 67.8767 | 13541 | 442 | 13543 | 669 | 329 | 49.1779 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 99.1054 | 98.7352 | 99.4784 | 63.8767 | 13583 | 174 | 13541 | 71 | 56 | 78.8732 | |
| jli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 99.1054 | 98.7352 | 99.4784 | 63.8767 | 13583 | 174 | 13541 | 71 | 56 | 78.8732 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.8269 | 98.7352 | 98.9188 | 69.0820 | 13583 | 174 | 13540 | 148 | 116 | 78.3784 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.8269 | 98.7352 | 98.9188 | 69.0820 | 13583 | 174 | 13540 | 148 | 116 | 78.3784 | |
| gduggal-bwavard | SNP | ti | map_l100_m0_e0 | het | 93.7781 | 97.4183 | 90.4002 | 80.9729 | 13622 | 361 | 13532 | 1437 | 84 | 5.8455 | |
| anovak-vg | SNP | ti | HG002compoundhet | * | 77.8164 | 75.3290 | 80.4737 | 38.3806 | 13166 | 4312 | 13522 | 3281 | 2578 | 78.5736 | |
| ltrigg-rtg2 | SNP | ti | map_l100_m0_e0 | het | 98.2231 | 96.6531 | 99.8449 | 50.2864 | 13515 | 468 | 13519 | 21 | 2 | 9.5238 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 86.2115 | 84.1466 | 88.3803 | 58.2216 | 13503 | 2544 | 13516 | 1777 | 1745 | 98.1992 | |
| astatham-gatk | SNP | tv | map_l125_m1_e0 | * | 91.3826 | 84.3531 | 99.6900 | 75.2873 | 13510 | 2506 | 13508 | 42 | 14 | 33.3333 | |
| jmaeng-gatk | SNP | ti | map_l100_m2_e0 | homalt | 84.8820 | 73.7670 | 99.9408 | 66.4315 | 13506 | 4803 | 13506 | 8 | 7 | 87.5000 | |
| qzeng-custom | SNP | * | map_l150_m1_e0 | het | 81.0937 | 70.5218 | 95.3942 | 89.4771 | 13622 | 5694 | 13504 | 652 | 548 | 84.0491 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.1543 | 98.3354 | 97.9739 | 68.1869 | 13528 | 229 | 13491 | 279 | 216 | 77.4194 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.1543 | 98.3354 | 97.9739 | 68.1869 | 13528 | 229 | 13491 | 279 | 216 | 77.4194 | |
| ciseli-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 76.1186 | 81.3959 | 71.4838 | 54.5214 | 12828 | 2932 | 13489 | 5381 | 2743 | 50.9757 | |
| anovak-vg | SNP | ti | func_cds | * | 98.6277 | 98.0852 | 99.1763 | 27.7317 | 13523 | 264 | 13486 | 112 | 79 | 70.5357 | |
| gduggal-snapvard | INDEL | I6_15 | * | * | 50.7754 | 45.6827 | 57.1459 | 41.2412 | 11338 | 13481 | 13483 | 10111 | 8109 | 80.1998 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 90.5625 | 95.5867 | 86.0400 | 54.3416 | 5588 | 258 | 13473 | 2186 | 990 | 45.2882 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 90.5625 | 95.5867 | 86.0400 | 54.3416 | 5588 | 258 | 13473 | 2186 | 990 | 45.2882 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 65.4735 | 66.2226 | 64.7412 | 60.6352 | 12030 | 6136 | 13472 | 7337 | 6068 | 82.7041 | |
| anovak-vg | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 65.4735 | 66.2226 | 64.7412 | 60.6352 | 12030 | 6136 | 13472 | 7337 | 6068 | 82.7041 | |
| ckim-isaac | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 91.1346 | 84.9322 | 98.3142 | 43.5277 | 13094 | 2323 | 13472 | 231 | 203 | 87.8788 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 97.0172 | 94.5909 | 99.5711 | 30.5429 | 13273 | 759 | 13466 | 58 | 56 | 96.5517 | |