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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
8251-8300 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.8690 | 98.8710 | 96.8872 | 72.0428 | 5780 | 66 | 5727 | 184 | 169 | 91.8478 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.8690 | 98.8710 | 96.8872 | 72.0428 | 5780 | 66 | 5727 | 184 | 169 | 91.8478 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.4118 | 97.6791 | 97.1460 | 75.4876 | 6271 | 149 | 6263 | 184 | 164 | 89.1304 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.4118 | 97.6791 | 97.1460 | 75.4876 | 6271 | 149 | 6263 | 184 | 164 | 89.1304 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 68.9517 | 64.3204 | 74.3017 | 60.0892 | 530 | 294 | 532 | 184 | 182 | 98.9130 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m1_e0 | * | 92.6870 | 95.1299 | 90.3665 | 86.2223 | 1758 | 90 | 1726 | 184 | 50 | 27.1739 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m2_e0 | * | 92.8526 | 95.1436 | 90.6694 | 86.8647 | 1822 | 93 | 1788 | 184 | 50 | 27.1739 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 33.8099 | 25.0000 | 52.2078 | 71.4603 | 209 | 627 | 201 | 184 | 169 | 91.8478 | |
| gduggal-bwavard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 87.0247 | 88.6166 | 85.4890 | 87.6172 | 1121 | 144 | 1084 | 184 | 65 | 35.3261 | |
| gduggal-bwafb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.5242 | 99.6649 | 93.5754 | 71.7749 | 2677 | 9 | 2680 | 184 | 9 | 4.8913 | |
| gduggal-bwafb | SNP | * | map_l150_m0_e0 | * | 98.2636 | 98.0635 | 98.4645 | 81.5621 | 11799 | 233 | 11799 | 184 | 58 | 31.5217 | |
| anovak-vg | INDEL | I1_5 | map_l100_m1_e0 | het | 47.9187 | 38.2239 | 64.2023 | 89.2961 | 297 | 480 | 330 | 184 | 31 | 16.8478 | |
| anovak-vg | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 67.1212 | 72.5490 | 62.4490 | 44.0639 | 111 | 42 | 306 | 184 | 163 | 88.5870 | |
| astatham-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.5706 | 99.1399 | 92.2494 | 66.0177 | 2190 | 19 | 2190 | 184 | 181 | 98.3696 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 92.2288 | 98.9002 | 86.4006 | 59.8278 | 1169 | 13 | 1169 | 184 | 183 | 99.4565 | |
| ciseli-custom | INDEL | I6_15 | HG002complexvar | het | 39.0345 | 26.1146 | 77.2559 | 60.9179 | 615 | 1740 | 625 | 184 | 138 | 75.0000 | |
| ciseli-custom | INDEL | D1_5 | map_l125_m2_e1 | * | 76.9744 | 72.4287 | 82.1289 | 90.9356 | 838 | 319 | 841 | 183 | 83 | 45.3552 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 26.6407 | 17.5625 | 55.1471 | 66.3088 | 232 | 1089 | 225 | 183 | 170 | 92.8962 | |
| ckim-dragen | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 95.3176 | 99.5904 | 91.3963 | 41.9328 | 1945 | 8 | 1944 | 183 | 182 | 99.4536 | |
| ckim-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3819 | 99.8008 | 98.9665 | 67.1777 | 17533 | 35 | 17523 | 183 | 15 | 8.1967 | |
| cchapple-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.9495 | 96.9056 | 99.0161 | 33.0779 | 17694 | 565 | 18416 | 183 | 178 | 97.2678 | |
| cchapple-custom | SNP | * | segdup | * | 99.5856 | 99.8219 | 99.3504 | 91.8828 | 28017 | 50 | 27988 | 183 | 25 | 13.6612 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.7733 | 97.4942 | 98.0540 | 45.3637 | 9221 | 237 | 9221 | 183 | 179 | 97.8142 | |
| ckim-vqsr | SNP | ti | map_l100_m1_e0 | het | 85.6453 | 75.3523 | 99.1953 | 82.9534 | 22562 | 7380 | 22557 | 183 | 10 | 5.4645 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 81.9533 | 97.9730 | 70.4362 | 86.4433 | 435 | 9 | 436 | 183 | 145 | 79.2350 | |
| qzeng-custom | SNP | tv | map_l150_m0_e0 | * | 79.1205 | 68.3277 | 93.9624 | 92.1942 | 2852 | 1322 | 2848 | 183 | 152 | 83.0601 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.5533 | 98.7871 | 98.3205 | 78.4263 | 10670 | 131 | 10713 | 183 | 3 | 1.6393 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.0864 | 98.7941 | 97.3887 | 79.6107 | 6800 | 83 | 6825 | 183 | 3 | 1.6393 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.2962 | 90.1200 | 96.7045 | 61.7457 | 5482 | 601 | 5370 | 183 | 171 | 93.4426 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.2283 | 95.5860 | 98.9279 | 54.0066 | 16891 | 780 | 16887 | 183 | 169 | 92.3497 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.2283 | 95.5860 | 98.9279 | 54.0066 | 16891 | 780 | 16887 | 183 | 169 | 92.3497 | |
| jlack-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0614 | 99.8136 | 98.3203 | 43.6922 | 10712 | 20 | 10712 | 183 | 5 | 2.7322 | |
| hfeng-pmm1 | INDEL | I1_5 | HG002compoundhet | * | 96.2606 | 94.1648 | 98.4519 | 64.4321 | 11635 | 721 | 11638 | 183 | 176 | 96.1749 | |
| jli-custom | INDEL | I6_15 | * | homalt | 98.3861 | 99.6634 | 97.1411 | 49.1984 | 6218 | 21 | 6218 | 183 | 180 | 98.3607 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.1115 | 96.7548 | 99.5067 | 50.1900 | 36672 | 1230 | 36914 | 183 | 147 | 80.3279 | |
| ghariani-varprowl | INDEL | * | map_l150_m2_e0 | * | 91.0274 | 94.3892 | 87.8968 | 95.3487 | 1329 | 79 | 1329 | 183 | 52 | 28.4153 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 92.8911 | 87.3497 | 99.1833 | 60.3693 | 22151 | 3208 | 22225 | 183 | 36 | 19.6721 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 29.0076 | 92.6829 | 17.1946 | 91.1987 | 38 | 3 | 38 | 183 | 8 | 4.3716 | |
| anovak-vg | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 51.7848 | 41.9187 | 67.7249 | 51.1628 | 402 | 557 | 384 | 183 | 140 | 76.5027 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 81.6794 | 97.9405 | 70.0491 | 45.2509 | 428 | 9 | 428 | 183 | 183 | 100.0000 | |
| gduggal-bwavard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 83.9654 | 89.6725 | 78.9413 | 89.5816 | 712 | 82 | 686 | 183 | 64 | 34.9727 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 60.9324 | 77.3279 | 50.2732 | 71.4953 | 191 | 56 | 184 | 182 | 167 | 91.7582 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 22.2368 | 13.7681 | 57.7726 | 41.9919 | 57 | 357 | 249 | 182 | 181 | 99.4505 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m1_e0 | het | 92.3518 | 98.9247 | 86.5979 | 88.3812 | 1196 | 13 | 1176 | 182 | 48 | 26.3736 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m2_e0 | het | 92.5331 | 98.8057 | 87.0093 | 88.9275 | 1241 | 15 | 1219 | 182 | 48 | 26.3736 | |
| jli-custom | INDEL | D1_5 | HG002compoundhet | * | 97.1251 | 95.8153 | 98.4712 | 65.0788 | 11723 | 512 | 11723 | 182 | 174 | 95.6044 | |
| jli-custom | INDEL | I1_5 | HG002compoundhet | * | 96.2734 | 94.1810 | 98.4609 | 66.0757 | 11637 | 719 | 11643 | 182 | 172 | 94.5055 | |
| jli-custom | SNP | * | segdup | * | 99.5966 | 99.8397 | 99.3547 | 89.2512 | 28022 | 45 | 28022 | 182 | 12 | 6.5934 | |
| ltrigg-rtg2 | SNP | tv | HG002complexvar | * | 99.8482 | 99.7705 | 99.9260 | 21.7021 | 245590 | 565 | 245834 | 182 | 72 | 39.5604 | |
| qzeng-custom | INDEL | D16_PLUS | HG002compoundhet | homalt | 6.1856 | 100.0000 | 3.1915 | 36.2712 | 8 | 0 | 6 | 182 | 92 | 50.5495 | |