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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
21151-21200 / 86044 show all | |||||||||||||||
| qzeng-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.2458 | 97.9315 | 96.5697 | 82.2940 | 19174 | 405 | 19284 | 685 | 59 | 8.6131 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.2451 | 95.3502 | 99.2167 | 55.7798 | 8018 | 391 | 8107 | 64 | 58 | 90.6250 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.2445 | 96.0604 | 98.4581 | 67.5236 | 17117 | 702 | 16730 | 262 | 221 | 84.3511 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.2443 | 95.7292 | 98.8082 | 63.2331 | 6052 | 270 | 6052 | 73 | 63 | 86.3014 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.2443 | 95.7292 | 98.8082 | 63.2331 | 6052 | 270 | 6052 | 73 | 63 | 86.3014 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.2439 | 97.3027 | 97.1852 | 57.6417 | 35605 | 987 | 38256 | 1108 | 730 | 65.8845 | |
| eyeh-varpipe | INDEL | * | map_l150_m0_e0 | homalt | 97.2434 | 98.1707 | 96.3333 | 91.9420 | 161 | 3 | 289 | 11 | 11 | 100.0000 | |
| ghariani-varprowl | INDEL | I1_5 | map_l150_m2_e0 | homalt | 97.2431 | 96.5174 | 97.9798 | 85.0114 | 194 | 7 | 194 | 4 | 2 | 50.0000 | |
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.2427 | 99.4993 | 95.0863 | 76.1894 | 16890 | 85 | 16913 | 874 | 433 | 49.5423 | |
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.2427 | 99.4993 | 95.0863 | 76.1894 | 16890 | 85 | 16913 | 874 | 433 | 49.5423 | |
| mlin-fermikit | INDEL | I1_5 | * | het | 97.2425 | 97.2166 | 97.2684 | 53.2963 | 76841 | 2200 | 76701 | 2154 | 2108 | 97.8644 | |
| astatham-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 97.2405 | 95.8549 | 98.6667 | 91.1368 | 370 | 16 | 370 | 5 | 3 | 60.0000 | |
| jmaeng-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 97.2405 | 95.8549 | 98.6667 | 91.0990 | 370 | 16 | 370 | 5 | 3 | 60.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.2401 | 95.3342 | 99.2238 | 23.4653 | 756 | 37 | 767 | 6 | 6 | 100.0000 | |
| jli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.2401 | 95.3342 | 99.2238 | 23.4653 | 756 | 37 | 767 | 6 | 5 | 83.3333 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 97.2401 | 97.2678 | 97.2125 | 76.6096 | 534 | 15 | 558 | 16 | 13 | 81.2500 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.2401 | 95.3342 | 99.2238 | 23.4653 | 756 | 37 | 767 | 6 | 6 | 100.0000 | |
| ciseli-custom | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 97.2393 | 99.5982 | 94.9895 | 38.3851 | 2727 | 11 | 2711 | 143 | 53 | 37.0629 | |
| eyeh-varpipe | INDEL | D1_5 | map_siren | * | 97.2391 | 97.2230 | 97.2552 | 80.6160 | 3431 | 98 | 3685 | 104 | 64 | 61.5385 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.2389 | 96.9229 | 97.5570 | 48.8051 | 10741 | 341 | 10742 | 269 | 266 | 98.8848 | |
| anovak-vg | SNP | ti | segdup | het | 97.2381 | 97.4480 | 97.0290 | 93.2429 | 11723 | 307 | 11659 | 357 | 90 | 25.2101 | |
| jli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.2379 | 97.0149 | 97.4619 | 86.3856 | 195 | 6 | 192 | 5 | 1 | 20.0000 | |
| raldana-dualsentieon | INDEL | * | map_l150_m2_e1 | * | 97.2377 | 96.5254 | 97.9606 | 88.6503 | 1389 | 50 | 1393 | 29 | 5 | 17.2414 | |
| hfeng-pmm2 | INDEL | D6_15 | segdup | het | 97.2376 | 95.6522 | 98.8764 | 94.8044 | 88 | 4 | 88 | 1 | 0 | 0.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.2376 | 96.9527 | 97.5243 | 55.9478 | 36747 | 1155 | 36556 | 928 | 901 | 97.0905 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l250_m2_e1 | * | 97.2376 | 95.1351 | 99.4350 | 94.2157 | 176 | 9 | 176 | 1 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | I1_5 | * | hetalt | 97.2375 | 95.2479 | 99.3119 | 61.7967 | 10663 | 532 | 10681 | 74 | 69 | 93.2432 | |
| ndellapenna-hhga | INDEL | * | map_l100_m2_e1 | het | 97.2372 | 97.3111 | 97.1634 | 84.0911 | 2280 | 63 | 2295 | 67 | 27 | 40.2985 | |
| anovak-vg | SNP | ti | HG002complexvar | het | 97.2372 | 96.4650 | 98.0220 | 17.7484 | 303639 | 11127 | 299610 | 6046 | 4694 | 77.6381 | |
| cchapple-custom | INDEL | D1_5 | map_l125_m0_e0 | homalt | 97.2366 | 95.2703 | 99.2857 | 85.6263 | 141 | 7 | 139 | 1 | 1 | 100.0000 | |
| astatham-gatk | INDEL | D6_15 | map_siren | * | 97.2363 | 96.8566 | 97.6190 | 85.4503 | 493 | 16 | 492 | 12 | 2 | 16.6667 | |
| qzeng-custom | INDEL | * | func_cds | homalt | 97.2362 | 99.5575 | 95.0207 | 31.7280 | 225 | 1 | 229 | 12 | 2 | 16.6667 | |
| ndellapenna-hhga | INDEL | * | map_l100_m2_e1 | * | 97.2360 | 96.8584 | 97.6165 | 97.7206 | 3638 | 118 | 3645 | 89 | 40 | 44.9438 | |
| jli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 97.2360 | 95.2999 | 99.2524 | 31.1832 | 1541 | 76 | 1726 | 13 | 13 | 100.0000 | |
| ckim-dragen | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.2357 | 94.9731 | 99.6087 | 58.9389 | 14642 | 775 | 14763 | 58 | 58 | 100.0000 | |
| gduggal-snapfb | SNP | * | map_l150_m2_e1 | homalt | 97.2353 | 95.0114 | 99.5658 | 80.8094 | 11237 | 590 | 11237 | 49 | 20 | 40.8163 | |
| ltrigg-rtg1 | INDEL | * | map_l125_m2_e0 | * | 97.2353 | 95.2641 | 99.2898 | 83.0932 | 2092 | 104 | 2097 | 15 | 3 | 20.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 97.2350 | 94.7249 | 99.8818 | 43.0518 | 3340 | 186 | 3381 | 4 | 4 | 100.0000 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 97.2350 | 94.7249 | 99.8818 | 43.0518 | 3340 | 186 | 3381 | 4 | 4 | 100.0000 | |
| ltrigg-rtg2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.2347 | 98.2481 | 96.2420 | 74.4091 | 8973 | 160 | 9117 | 356 | 12 | 3.3708 | |
| ltrigg-rtg2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.2347 | 98.2481 | 96.2420 | 74.4091 | 8973 | 160 | 9117 | 356 | 12 | 3.3708 | |
| ltrigg-rtg2 | INDEL | I1_5 | map_l125_m2_e0 | het | 97.2343 | 95.5734 | 98.9540 | 80.5770 | 475 | 22 | 473 | 5 | 0 | 0.0000 | |
| astatham-gatk | INDEL | D1_5 | * | hetalt | 97.2343 | 95.0220 | 99.5520 | 63.2355 | 9735 | 510 | 9778 | 44 | 43 | 97.7273 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 97.2341 | 94.6563 | 99.9563 | 27.5665 | 4517 | 255 | 4570 | 2 | 2 | 100.0000 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 97.2339 | 99.3295 | 95.2250 | 57.6340 | 11407 | 77 | 11407 | 572 | 562 | 98.2517 | |
| ltrigg-rtg1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.2339 | 95.3125 | 99.2344 | 58.7664 | 1708 | 84 | 1685 | 13 | 10 | 76.9231 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.2332 | 96.8504 | 97.6190 | 78.9649 | 123 | 4 | 123 | 3 | 2 | 66.6667 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.2332 | 96.8504 | 97.6190 | 78.7879 | 123 | 4 | 123 | 3 | 2 | 66.6667 | |
| hfeng-pmm1 | INDEL | D6_15 | map_l100_m1_e0 | het | 97.2332 | 97.6190 | 96.8504 | 86.2256 | 123 | 3 | 123 | 4 | 1 | 25.0000 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.2332 | 96.8504 | 97.6190 | 80.0633 | 123 | 4 | 123 | 3 | 2 | 66.6667 | |