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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
33201-33250 / 86044 show all | |||||||||||||||
| gduggal-snapvard | INDEL | * | map_l125_m1_e0 | * | 85.8371 | 91.9791 | 80.4640 | 88.3383 | 1938 | 169 | 2636 | 640 | 251 | 39.2188 | |
| mlin-fermikit | SNP | * | HG002compoundhet | * | 92.7673 | 91.9758 | 93.5725 | 42.5829 | 23750 | 2072 | 23759 | 1632 | 1332 | 81.6176 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 60.0589 | 91.9736 | 44.5872 | 75.8345 | 1673 | 146 | 1701 | 2114 | 1899 | 89.8297 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 60.0589 | 91.9736 | 44.5872 | 75.8345 | 1673 | 146 | 1701 | 2114 | 1899 | 89.8297 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 95.0667 | 91.9708 | 98.3784 | 71.2062 | 378 | 33 | 364 | 6 | 5 | 83.3333 | |
| raldana-dualsentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 95.8057 | 91.9684 | 99.9771 | 32.4064 | 12905 | 1127 | 13098 | 3 | 3 | 100.0000 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 94.8405 | 91.9659 | 97.9006 | 68.3752 | 18006 | 1573 | 18000 | 386 | 15 | 3.8860 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 94.8405 | 91.9659 | 97.9006 | 68.3752 | 18006 | 1573 | 18000 | 386 | 15 | 3.8860 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 95.8140 | 91.9643 | 100.0000 | 71.8579 | 103 | 9 | 103 | 0 | 0 | ||
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 95.8140 | 91.9643 | 100.0000 | 71.9346 | 103 | 9 | 103 | 0 | 0 | ||
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 95.8140 | 91.9643 | 100.0000 | 71.9346 | 103 | 9 | 103 | 0 | 0 | ||
| jli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 95.1323 | 91.9608 | 98.5304 | 80.4728 | 1407 | 123 | 1408 | 21 | 9 | 42.8571 | |
| jli-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 95.1323 | 91.9608 | 98.5304 | 80.4728 | 1407 | 123 | 1408 | 21 | 9 | 42.8571 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.7952 | 91.9607 | 99.9635 | 35.1166 | 5422 | 474 | 5480 | 2 | 2 | 100.0000 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.7952 | 91.9607 | 99.9635 | 35.1166 | 5422 | 474 | 5480 | 2 | 2 | 100.0000 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 92.5879 | 91.9586 | 93.2258 | 73.3046 | 1155 | 101 | 1156 | 84 | 55 | 65.4762 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 95.7931 | 91.9551 | 99.9655 | 41.6230 | 2869 | 251 | 2898 | 1 | 1 | 100.0000 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 95.2451 | 91.9540 | 98.7805 | 77.4105 | 80 | 7 | 81 | 1 | 1 | 100.0000 | |
| jmaeng-gatk | INDEL | D16_PLUS | map_l100_m1_e0 | * | 88.8889 | 91.9540 | 86.0215 | 94.9264 | 80 | 7 | 80 | 13 | 4 | 30.7692 | |
| jpowers-varprowl | INDEL | I1_5 | map_l125_m2_e1 | * | 94.1730 | 91.9540 | 96.5018 | 87.3047 | 800 | 70 | 800 | 29 | 21 | 72.4138 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 93.5396 | 91.9540 | 95.1807 | 99.8985 | 80 | 7 | 79 | 4 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 93.5396 | 91.9540 | 95.1807 | 99.8965 | 80 | 7 | 79 | 4 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | map_l100_m1_e0 | * | 89.8876 | 91.9540 | 87.9121 | 95.3737 | 80 | 7 | 80 | 11 | 4 | 36.3636 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 95.2451 | 91.9540 | 98.7805 | 76.3006 | 80 | 7 | 81 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 93.5396 | 91.9540 | 95.1807 | 99.8945 | 80 | 7 | 79 | 4 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | D16_PLUS | map_l100_m1_e0 | * | 87.4317 | 91.9540 | 83.3333 | 94.2618 | 80 | 7 | 80 | 16 | 4 | 25.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | map_l100_m1_e0 | * | 89.8876 | 91.9540 | 87.9121 | 92.2421 | 80 | 7 | 80 | 11 | 2 | 18.1818 | |
| hfeng-pmm2 | INDEL | D16_PLUS | map_l100_m1_e0 | * | 88.3978 | 91.9540 | 85.1064 | 93.2713 | 80 | 7 | 80 | 14 | 3 | 21.4286 | |
| ckim-gatk | INDEL | D16_PLUS | map_l100_m1_e0 | * | 89.3855 | 91.9540 | 86.9565 | 95.3252 | 80 | 7 | 80 | 12 | 4 | 33.3333 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 95.7068 | 91.9529 | 99.7804 | 63.8066 | 15609 | 1366 | 15447 | 34 | 16 | 47.0588 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 95.7068 | 91.9529 | 99.7804 | 63.8066 | 15609 | 1366 | 15447 | 34 | 16 | 47.0588 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.7859 | 91.9518 | 99.9537 | 23.9402 | 4273 | 374 | 4322 | 2 | 2 | 100.0000 | |
| qzeng-custom | INDEL | D16_PLUS | * | * | 79.4045 | 91.9517 | 69.8705 | 62.5471 | 6238 | 546 | 6528 | 2815 | 413 | 14.6714 | |
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.0121 | 91.9517 | 98.2833 | 74.7972 | 457 | 40 | 458 | 8 | 6 | 75.0000 | |
| jpowers-varprowl | INDEL | I1_5 | map_l125_m2_e0 | * | 94.2020 | 91.9487 | 96.5686 | 87.1557 | 788 | 69 | 788 | 28 | 21 | 75.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 93.2618 | 91.9463 | 94.6154 | 77.5475 | 137 | 12 | 123 | 7 | 5 | 71.4286 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 77.4574 | 91.9436 | 66.9147 | 52.7787 | 3458 | 303 | 6476 | 3202 | 3147 | 98.2823 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 77.4574 | 91.9436 | 66.9147 | 52.7787 | 3458 | 303 | 6476 | 3202 | 3147 | 98.2823 | |
| ltrigg-rtg1 | INDEL | * | map_l150_m2_e0 | het | 95.3640 | 91.9426 | 99.0499 | 82.6284 | 833 | 73 | 834 | 8 | 0 | 0.0000 | |
| cchapple-custom | INDEL | I16_PLUS | HG002complexvar | hetalt | 0.0000 | 91.9403 | 0.0000 | 0.0000 | 308 | 27 | 0 | 0 | 0 | ||
| gduggal-bwavard | INDEL | * | map_siren | homalt | 95.6313 | 91.9397 | 99.6318 | 70.4973 | 2441 | 214 | 2435 | 9 | 6 | 66.6667 | |
| jpowers-varprowl | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 89.8707 | 91.9395 | 87.8929 | 91.5916 | 730 | 64 | 755 | 104 | 4 | 3.8462 | |
| rpoplin-dv42 | INDEL | D1_5 | HG002complexvar | hetalt | 94.1845 | 91.9379 | 96.5438 | 71.6833 | 1243 | 109 | 1257 | 45 | 44 | 97.7778 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 94.5299 | 91.9369 | 97.2735 | 78.9642 | 1049 | 92 | 1213 | 34 | 29 | 85.2941 | |
| jpowers-varprowl | INDEL | I1_5 | map_l125_m0_e0 | * | 94.3709 | 91.9355 | 96.9388 | 89.0052 | 285 | 25 | 285 | 9 | 6 | 66.6667 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 95.5307 | 91.9355 | 99.4186 | 70.2936 | 171 | 15 | 171 | 1 | 1 | 100.0000 | |
| ckim-isaac | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.5412 | 91.9336 | 99.4434 | 50.8361 | 1607 | 141 | 1608 | 9 | 7 | 77.7778 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 95.6093 | 91.9316 | 99.5935 | 30.0616 | 10209 | 896 | 10290 | 42 | 37 | 88.0952 | |
| jpowers-varprowl | INDEL | * | map_l100_m1_e0 | homalt | 95.3105 | 91.9315 | 98.9474 | 78.3927 | 1128 | 99 | 1128 | 12 | 8 | 66.6667 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 95.4239 | 91.9294 | 99.1946 | 24.7475 | 729 | 64 | 739 | 6 | 6 | 100.0000 | |