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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
30401-30450 / 86044 show all | |||||||||||||||
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 93.2788 | 89.2617 | 97.6744 | 69.3587 | 133 | 16 | 126 | 3 | 1 | 33.3333 | |
| jpowers-varprowl | INDEL | D1_5 | map_l250_m2_e0 | het | 93.2773 | 91.7355 | 94.8718 | 96.5022 | 111 | 10 | 111 | 6 | 3 | 50.0000 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 93.2767 | 96.0630 | 90.6475 | 74.0187 | 122 | 5 | 126 | 13 | 7 | 53.8462 | |
| gduggal-snapplat | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 93.2764 | 88.2353 | 98.9284 | 63.4212 | 9780 | 1304 | 9786 | 106 | 22 | 20.7547 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.2754 | 89.6920 | 97.1571 | 51.8026 | 3524 | 405 | 3520 | 103 | 96 | 93.2039 | |
| jmaeng-gatk | INDEL | * | map_l250_m2_e1 | * | 93.2749 | 95.7958 | 90.8832 | 97.4381 | 319 | 14 | 319 | 32 | 4 | 12.5000 | |
| jmaeng-gatk | INDEL | I1_5 | segdup | het | 93.2743 | 99.0706 | 88.1188 | 96.5876 | 533 | 5 | 534 | 72 | 0 | 0.0000 | |
| rpoplin-dv42 | INDEL | I6_15 | map_l100_m2_e0 | * | 93.2735 | 89.6552 | 97.1963 | 85.5014 | 104 | 12 | 104 | 3 | 2 | 66.6667 | |
| rpoplin-dv42 | INDEL | I6_15 | map_l100_m2_e1 | * | 93.2735 | 89.6552 | 97.1963 | 85.8466 | 104 | 12 | 104 | 3 | 2 | 66.6667 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | het | 93.2727 | 93.4426 | 93.1034 | 80.4054 | 57 | 4 | 54 | 4 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.2704 | 87.7615 | 99.5173 | 36.9269 | 3356 | 468 | 3505 | 17 | 17 | 100.0000 | |
| ckim-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.2704 | 87.7615 | 99.5173 | 36.9269 | 3356 | 468 | 3505 | 17 | 17 | 100.0000 | |
| gduggal-snapplat | SNP | ti | map_l150_m2_e0 | homalt | 93.2670 | 87.4869 | 99.8649 | 73.8706 | 6663 | 953 | 6654 | 9 | 9 | 100.0000 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 93.2666 | 89.8204 | 96.9880 | 69.6527 | 150 | 17 | 161 | 5 | 5 | 100.0000 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 93.2663 | 94.0755 | 92.4709 | 53.9758 | 9575 | 603 | 9543 | 777 | 701 | 90.2188 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 93.2644 | 90.8623 | 95.7970 | 33.1527 | 18714 | 1882 | 18667 | 819 | 734 | 89.6215 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.2637 | 97.8947 | 89.0511 | 87.2350 | 651 | 14 | 488 | 60 | 49 | 81.6667 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 93.2622 | 98.0574 | 88.9141 | 86.8298 | 2322 | 46 | 2350 | 293 | 14 | 4.7782 | |
| 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 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.2615 | 97.1904 | 89.6378 | 74.6299 | 934 | 27 | 891 | 103 | 93 | 90.2913 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 93.2605 | 87.6033 | 99.6988 | 46.7095 | 318 | 45 | 331 | 1 | 1 | 100.0000 | |
| gduggal-bwavard | INDEL | I1_5 | map_l150_m1_e0 | het | 93.2578 | 98.3278 | 88.6850 | 92.8163 | 294 | 5 | 290 | 37 | 13 | 35.1351 | |
| ltrigg-rtg1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 93.2553 | 90.5797 | 96.0938 | 89.2437 | 250 | 26 | 246 | 10 | 1 | 10.0000 | |
| eyeh-varpipe | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.2516 | 98.6776 | 88.3913 | 75.0612 | 4701 | 63 | 4500 | 591 | 44 | 7.4450 | |
| hfeng-pmm3 | INDEL | * | map_l250_m0_e0 | * | 93.2515 | 97.4359 | 89.4118 | 97.2159 | 76 | 2 | 76 | 9 | 2 | 22.2222 | |
| gduggal-snapplat | SNP | tv | map_l125_m1_e0 | * | 93.2502 | 91.0465 | 95.5633 | 81.8317 | 14582 | 1434 | 14582 | 677 | 351 | 51.8464 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 93.2492 | 92.4528 | 94.0594 | 60.0791 | 49 | 4 | 95 | 6 | 1 | 16.6667 | |
| cchapple-custom | INDEL | I1_5 | map_l250_m1_e0 | * | 93.2492 | 92.4528 | 94.0594 | 95.6068 | 98 | 8 | 95 | 6 | 1 | 16.6667 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 93.2488 | 96.4929 | 90.2158 | 52.0822 | 3054 | 111 | 3052 | 331 | 137 | 41.3897 | |
| ghariani-varprowl | INDEL | * | HG002complexvar | het | 93.2466 | 97.4941 | 89.3538 | 59.7893 | 45053 | 1158 | 45020 | 5364 | 4472 | 83.3706 | |
| jlack-gatk | INDEL | I1_5 | map_l150_m2_e1 | het | 93.2461 | 97.4763 | 89.3678 | 93.8559 | 309 | 8 | 311 | 37 | 2 | 5.4054 | |
| jlack-gatk | SNP | * | map_l250_m1_e0 | * | 93.2444 | 97.7569 | 89.1302 | 92.5027 | 7060 | 162 | 7060 | 861 | 66 | 7.6655 | |
| asubramanian-gatk | INDEL | I6_15 | map_l100_m2_e1 | * | 93.2442 | 88.7931 | 98.1651 | 89.8793 | 103 | 13 | 107 | 2 | 1 | 50.0000 | |
| gduggal-snapplat | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 93.2439 | 87.5263 | 99.7608 | 37.2372 | 1249 | 178 | 1251 | 3 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | * | 93.2432 | 92.0000 | 94.5205 | 64.5631 | 69 | 6 | 69 | 4 | 3 | 75.0000 | |
| gduggal-bwavard | SNP | * | tech_badpromoters | het | 93.2432 | 89.6104 | 97.1831 | 51.0345 | 69 | 8 | 69 | 2 | 1 | 50.0000 | |
| ckim-isaac | SNP | * | tech_badpromoters | * | 93.2432 | 87.8981 | 99.2806 | 31.5271 | 138 | 19 | 138 | 1 | 0 | 0.0000 | |
| eyeh-varpipe | INDEL | D6_15 | map_l125_m1_e0 | het | 93.2430 | 96.8750 | 89.8734 | 86.2609 | 62 | 2 | 71 | 8 | 8 | 100.0000 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 93.2428 | 98.0451 | 88.8889 | 87.2266 | 652 | 13 | 488 | 61 | 51 | 83.6066 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 93.2394 | 90.3138 | 96.3610 | 69.7623 | 662 | 71 | 662 | 25 | 18 | 72.0000 | |
| gduggal-bwafb | INDEL | D6_15 | HG002complexvar | * | 93.2387 | 90.0604 | 96.6496 | 53.7803 | 4775 | 527 | 4904 | 170 | 143 | 84.1176 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 93.2379 | 87.4049 | 99.9050 | 31.0740 | 2068 | 298 | 2103 | 2 | 2 | 100.0000 | |
| raldana-dualsentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 93.2373 | 98.5618 | 88.4586 | 59.3016 | 1165 | 17 | 1165 | 152 | 150 | 98.6842 | |
| asubramanian-gatk | INDEL | I6_15 | map_l100_m2_e0 | * | 93.2365 | 88.7931 | 98.1481 | 89.7045 | 103 | 13 | 106 | 2 | 1 | 50.0000 | |
| jmaeng-gatk | INDEL | * | map_l250_m2_e0 | * | 93.2353 | 95.7704 | 90.8309 | 97.3828 | 317 | 14 | 317 | 32 | 4 | 12.5000 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | map_siren | het | 93.2340 | 88.4615 | 98.5507 | 87.7876 | 69 | 9 | 68 | 1 | 0 | 0.0000 | |
| ndellapenna-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 93.2318 | 91.4352 | 95.1004 | 84.7221 | 1185 | 111 | 1184 | 61 | 36 | 59.0164 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.2315 | 88.9794 | 97.9104 | 67.2852 | 1639 | 203 | 1640 | 35 | 28 | 80.0000 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 93.2309 | 99.3718 | 87.8049 | 80.7052 | 19456 | 123 | 18720 | 2600 | 87 | 3.3462 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 93.2309 | 99.3718 | 87.8049 | 80.7052 | 19456 | 123 | 18720 | 2600 | 87 | 3.3462 | |