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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
60751-60800 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.4879 | 96.2662 | 96.7105 | 67.7111 | 593 | 23 | 588 | 20 | 18 | 90.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | map_l100_m2_e1 | * | 79.6555 | 76.2887 | 83.3333 | 87.4652 | 74 | 23 | 75 | 15 | 11 | 73.3333 | |
| egarrison-hhga | INDEL | D1_5 | map_siren | het | 98.6006 | 98.9899 | 98.2143 | 79.8047 | 2254 | 23 | 2255 | 41 | 14 | 34.1463 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.4202 | 96.3492 | 96.4912 | 68.0265 | 607 | 23 | 605 | 22 | 7 | 31.8182 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 90.5056 | 92.0139 | 89.0459 | 72.4440 | 265 | 23 | 252 | 31 | 15 | 48.3871 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 96.1650 | 95.9220 | 96.4093 | 67.7662 | 541 | 23 | 537 | 20 | 9 | 45.0000 | |
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 95.4649 | 94.8198 | 96.1187 | 82.0271 | 421 | 23 | 421 | 17 | 14 | 82.3529 | |
| egarrison-hhga | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.6106 | 99.4231 | 99.7987 | 35.5602 | 3964 | 23 | 3966 | 8 | 6 | 75.0000 | |
| egarrison-hhga | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.7861 | 99.6723 | 99.9000 | 60.2486 | 6996 | 23 | 6996 | 7 | 5 | 71.4286 | |
| egarrison-hhga | SNP | tv | map_l250_m0_e0 | het | 97.4268 | 95.9790 | 98.9189 | 91.9902 | 549 | 23 | 549 | 6 | 2 | 33.3333 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.1228 | 96.5257 | 97.7273 | 78.8316 | 639 | 23 | 602 | 14 | 8 | 57.1429 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.0855 | 99.3885 | 98.7844 | 71.5296 | 3738 | 23 | 3738 | 46 | 44 | 95.6522 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.0855 | 99.3885 | 98.7844 | 71.5296 | 3738 | 23 | 3738 | 46 | 44 | 95.6522 | |
| dgrover-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.9859 | 98.8636 | 99.1085 | 68.8570 | 2001 | 23 | 2001 | 18 | 6 | 33.3333 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 95.1367 | 94.4039 | 95.8810 | 72.5157 | 388 | 23 | 419 | 18 | 18 | 100.0000 | |
| ckim-isaac | INDEL | D1_5 | segdup | * | 98.5851 | 97.9148 | 99.2647 | 92.9825 | 1080 | 23 | 1080 | 8 | 3 | 37.5000 | |
| ckim-isaac | INDEL | I1_5 | map_l250_m1_e0 | homalt | 64.6154 | 47.7273 | 100.0000 | 93.0233 | 21 | 23 | 21 | 0 | 0 | ||
| ckim-isaac | INDEL | I1_5 | map_l250_m2_e0 | homalt | 65.6716 | 48.8889 | 100.0000 | 94.1176 | 22 | 23 | 22 | 0 | 0 | ||
| ckim-isaac | INDEL | I1_5 | map_l250_m2_e1 | homalt | 66.6667 | 50.0000 | 100.0000 | 94.0568 | 23 | 23 | 23 | 0 | 0 | ||
| ckim-vqsr | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.8966 | 96.4615 | 99.3750 | 22.2357 | 627 | 23 | 636 | 4 | 4 | 100.0000 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.4656 | 94.7248 | 98.2716 | 85.9667 | 413 | 23 | 398 | 7 | 5 | 71.4286 | |
| ckim-vqsr | INDEL | I1_5 | map_l150_m2_e0 | * | 96.5943 | 95.5684 | 97.6424 | 93.2903 | 496 | 23 | 497 | 12 | 2 | 16.6667 | |
| ckim-vqsr | INDEL | I1_5 | map_l150_m2_e1 | het | 94.6912 | 92.7445 | 96.7213 | 94.6529 | 294 | 23 | 295 | 10 | 1 | 10.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 83.4015 | 72.2892 | 98.5507 | 28.8660 | 60 | 23 | 68 | 1 | 1 | 100.0000 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.6636 | 99.5017 | 99.8260 | 39.5847 | 4593 | 23 | 4589 | 8 | 3 | 37.5000 | |
| ckim-vqsr | SNP | * | map_l125_m1_e0 | hetalt | 37.8378 | 23.3333 | 100.0000 | 96.4467 | 7 | 23 | 7 | 0 | 0 | ||
| ckim-vqsr | SNP | * | map_l125_m2_e0 | hetalt | 37.8378 | 23.3333 | 100.0000 | 97.1074 | 7 | 23 | 7 | 0 | 0 | ||
| ckim-vqsr | SNP | * | map_l125_m2_e1 | hetalt | 37.8378 | 23.3333 | 100.0000 | 97.1074 | 7 | 23 | 7 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.2430 | 99.1304 | 99.3558 | 84.2935 | 2622 | 23 | 2622 | 17 | 7 | 41.1765 | |
| ckim-vqsr | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.2513 | 99.5095 | 97.0246 | 43.7566 | 4666 | 23 | 4663 | 143 | 1 | 0.6993 | |
| ckim-vqsr | SNP | tv | map_l125_m1_e0 | hetalt | 37.8378 | 23.3333 | 100.0000 | 96.4467 | 7 | 23 | 7 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | map_l125_m2_e0 | hetalt | 37.8378 | 23.3333 | 100.0000 | 97.1074 | 7 | 23 | 7 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | map_l125_m2_e1 | hetalt | 37.8378 | 23.3333 | 100.0000 | 97.1074 | 7 | 23 | 7 | 0 | 0 | ||
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5603 | 99.5507 | 99.5700 | 75.2360 | 5096 | 23 | 5094 | 22 | 10 | 45.4545 | |
| dgrover-gatk | INDEL | D16_PLUS | HG002complexvar | hetalt | 93.7238 | 90.6883 | 96.9697 | 48.0899 | 224 | 23 | 448 | 14 | 14 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m2_e0 | * | 98.8260 | 98.7990 | 98.8530 | 85.3498 | 1892 | 23 | 1896 | 22 | 5 | 22.7273 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m2_e1 | * | 98.8405 | 98.8138 | 98.8671 | 85.4314 | 1916 | 23 | 1920 | 22 | 5 | 22.7273 | |
| ckim-isaac | INDEL | I6_15 | segdup | * | 91.8429 | 86.8571 | 97.4359 | 90.7253 | 152 | 23 | 152 | 4 | 3 | 75.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 97.0472 | 97.6240 | 96.4773 | 83.0378 | 945 | 23 | 849 | 31 | 21 | 67.7419 | |
| ckim-vqsr | INDEL | * | map_l125_m0_e0 | * | 96.5169 | 97.3923 | 95.6570 | 93.0361 | 859 | 23 | 859 | 39 | 4 | 10.2564 | |
| ckim-vqsr | INDEL | D16_PLUS | * | het | 97.9651 | 99.2719 | 96.6923 | 79.4267 | 3136 | 23 | 2894 | 99 | 69 | 69.6970 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 64.0961 | 94.0104 | 48.6239 | 70.6199 | 361 | 23 | 371 | 392 | 15 | 3.8265 | |
| qzeng-custom | INDEL | D6_15 | map_siren | het | 82.9558 | 91.7857 | 75.6757 | 84.8504 | 257 | 23 | 364 | 117 | 17 | 14.5299 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 85.0650 | 84.5638 | 85.5721 | 60.8569 | 126 | 23 | 344 | 58 | 50 | 86.2069 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 88.7085 | 94.0415 | 83.9479 | 92.5405 | 363 | 23 | 387 | 74 | 11 | 14.8649 | |
| qzeng-custom | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.1050 | 99.5095 | 94.8139 | 49.1046 | 4666 | 23 | 4662 | 255 | 3 | 1.1765 | |
| raldana-dualsentieon | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.2713 | 98.9588 | 91.8487 | 64.7877 | 2186 | 23 | 2186 | 194 | 191 | 98.4536 | |
| raldana-dualsentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.5713 | 99.3652 | 99.7783 | 74.4113 | 3600 | 23 | 3600 | 8 | 6 | 75.0000 | |
| raldana-dualsentieon | INDEL | * | map_l125_m0_e0 | het | 96.4980 | 96.0818 | 96.9178 | 87.6192 | 564 | 23 | 566 | 18 | 0 | 0.0000 | |
| raldana-dualsentieon | INDEL | * | map_siren | hetalt | 95.1168 | 90.6883 | 100.0000 | 85.1022 | 224 | 23 | 226 | 0 | 0 | ||