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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
6651-6700 / 86044 show all | |||||||||||||||
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 21.8945 | 17.7898 | 28.4615 | 75.2538 | 132 | 610 | 111 | 279 | 3 | 1.0753 | |
| qzeng-custom | SNP | tv | map_l150_m1_e0 | * | 82.5382 | 72.0674 | 96.5687 | 86.5523 | 7864 | 3048 | 7852 | 279 | 236 | 84.5878 | |
| qzeng-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 94.4318 | 96.0944 | 92.8258 | 50.7186 | 3543 | 144 | 3597 | 278 | 63 | 22.6619 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 77.9097 | 64.7065 | 97.8826 | 70.2472 | 12852 | 7010 | 12851 | 278 | 98 | 35.2518 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 86.1916 | 81.4378 | 91.5347 | 58.1069 | 2900 | 661 | 3006 | 278 | 275 | 98.9209 | |
| ckim-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.9363 | 99.2849 | 98.5900 | 75.9853 | 19439 | 140 | 19439 | 278 | 23 | 8.2734 | |
| ckim-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.9363 | 99.2849 | 98.5900 | 75.9853 | 19439 | 140 | 19439 | 278 | 23 | 8.2734 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.4677 | 98.0807 | 98.8578 | 41.0102 | 24069 | 471 | 24060 | 278 | 268 | 96.4029 | |
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 88.9231 | 98.9002 | 80.7746 | 59.1871 | 1169 | 13 | 1168 | 278 | 276 | 99.2806 | |
| anovak-vg | INDEL | * | map_l125_m0_e0 | * | 71.3287 | 72.2222 | 70.4570 | 90.6359 | 637 | 245 | 663 | 278 | 156 | 56.1151 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5115 | 98.1663 | 98.8593 | 41.0712 | 24090 | 450 | 24092 | 278 | 270 | 97.1223 | |
| rpoplin-dv42 | SNP | * | map_l100_m2_e0 | het | 99.2759 | 99.1530 | 99.3992 | 65.9847 | 46006 | 393 | 45994 | 278 | 141 | 50.7194 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 81.0483 | 98.1785 | 69.0078 | 78.8892 | 539 | 10 | 619 | 278 | 189 | 67.9856 | |
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 71.8992 | 96.8668 | 57.1649 | 88.9701 | 371 | 12 | 371 | 278 | 23 | 8.2734 | |
| hfeng-pmm1 | SNP | tv | * | * | 99.9383 | 99.9053 | 99.9713 | 20.8629 | 968772 | 918 | 968691 | 278 | 43 | 15.4676 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.0288 | 97.3348 | 98.7327 | 54.0492 | 21657 | 593 | 21658 | 278 | 267 | 96.0432 | |
| ckim-vqsr | SNP | * | map_l125_m1_e0 | * | 69.8181 | 53.9590 | 98.8800 | 88.0425 | 24458 | 20869 | 24455 | 277 | 5 | 1.8051 | |
| eyeh-varpipe | SNP | tv | HG002compoundhet | het | 92.5346 | 98.5876 | 87.1819 | 61.1401 | 4607 | 66 | 1884 | 277 | 44 | 15.8845 | |
| gduggal-bwafb | SNP | tv | HG002compoundhet | het | 96.4922 | 98.6946 | 94.3859 | 59.0165 | 4612 | 61 | 4657 | 277 | 52 | 18.7726 | |
| eyeh-varpipe | INDEL | I6_15 | HG002complexvar | homalt | 78.9714 | 80.2306 | 77.7510 | 38.7303 | 974 | 240 | 968 | 277 | 275 | 99.2780 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.0742 | 98.7301 | 99.4207 | 71.8442 | 47658 | 613 | 47540 | 277 | 83 | 29.9639 | |
| qzeng-custom | INDEL | C16_PLUS | * | het | 0.0000 | 0.0000 | 1.7730 | 70.9278 | 0 | 0 | 5 | 277 | 0 | 0.0000 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 82.5216 | 75.5967 | 90.8430 | 68.5420 | 2692 | 869 | 2748 | 277 | 196 | 70.7581 | |
| ckim-gatk | SNP | ti | map_l150_m1_e0 | * | 80.5127 | 68.3289 | 97.9843 | 87.5524 | 13469 | 6243 | 13465 | 277 | 34 | 12.2744 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 58.1410 | 81.6327 | 45.1485 | 57.8816 | 400 | 90 | 228 | 277 | 270 | 97.4729 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.1966 | 96.0492 | 98.3718 | 68.1010 | 17115 | 704 | 16736 | 277 | 229 | 82.6715 | |
| rpoplin-dv42 | SNP | * | map_l100_m1_e0 | het | 99.2638 | 99.1402 | 99.3876 | 64.2170 | 44969 | 390 | 44957 | 277 | 141 | 50.9025 | |
| raldana-dualsentieon | SNP | ti | map_l125_m2_e1 | het | 98.7395 | 98.9207 | 98.5590 | 73.8046 | 18881 | 206 | 18877 | 276 | 3 | 1.0870 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 89.5692 | 87.1711 | 92.1030 | 51.3163 | 3214 | 473 | 3219 | 276 | 266 | 96.3768 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 86.4923 | 90.0065 | 83.2423 | 70.9011 | 1387 | 154 | 1371 | 276 | 273 | 98.9130 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 87.3389 | 97.3404 | 79.2012 | 38.5364 | 183 | 5 | 1051 | 276 | 265 | 96.0145 | |
| qzeng-custom | SNP | tv | map_l125_m1_e0 | het | 85.2256 | 76.2789 | 96.5500 | 86.2555 | 7724 | 2402 | 7724 | 276 | 229 | 82.9710 | |
| gduggal-bwafb | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.0758 | 97.7052 | 94.4998 | 74.6425 | 4726 | 111 | 4742 | 276 | 80 | 28.9855 | |
| gduggal-bwafb | SNP | ti | map_l125_m1_e0 | het | 98.5889 | 98.6861 | 98.4920 | 74.2606 | 18026 | 240 | 18026 | 276 | 77 | 27.8986 | |
| egarrison-hhga | INDEL | D16_PLUS | HG002compoundhet | * | 61.7860 | 49.7651 | 81.4641 | 41.2623 | 1165 | 1176 | 1213 | 276 | 256 | 92.7536 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.0559 | 96.7947 | 99.3503 | 55.8922 | 41946 | 1389 | 42206 | 276 | 166 | 60.1449 | |
| jmaeng-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.0878 | 99.0624 | 99.1133 | 72.7315 | 30851 | 292 | 30851 | 276 | 26 | 9.4203 | |
| jmaeng-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.0878 | 99.0624 | 99.1133 | 72.7315 | 30851 | 292 | 30851 | 276 | 26 | 9.4203 | |
| hfeng-pmm3 | SNP | tv | * | * | 99.9443 | 99.9171 | 99.9715 | 21.1004 | 968886 | 804 | 968804 | 276 | 31 | 11.2319 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.2063 | 99.6651 | 96.7896 | 65.1548 | 8332 | 28 | 8321 | 276 | 275 | 99.6377 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.2063 | 99.6651 | 96.7896 | 65.1548 | 8332 | 28 | 8321 | 276 | 275 | 99.6377 | |
| ckim-dragen | SNP | tv | map_l150_m2_e0 | * | 98.2503 | 98.9080 | 97.6013 | 79.0121 | 11231 | 124 | 11230 | 276 | 27 | 9.7826 | |
| gduggal-snapvard | INDEL | C6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 56.8750 | 100.0000 | 39.7380 | 88.6830 | 1 | 0 | 182 | 276 | 65 | 23.5507 | |
| gduggal-snapvard | INDEL | C6_15 | HG002compoundhet | het | 0.0000 | 0.0000 | 25.8760 | 72.2513 | 0 | 0 | 96 | 275 | 70 | 25.4545 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 13.8244 | 10.6122 | 19.8251 | 85.5882 | 52 | 438 | 68 | 275 | 74 | 26.9091 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 49.9128 | 37.3964 | 75.0227 | 61.0403 | 902 | 1510 | 826 | 275 | 49 | 17.8182 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 91.5045 | 85.7025 | 98.1490 | 78.6703 | 14548 | 2427 | 14582 | 275 | 104 | 37.8182 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 91.5045 | 85.7025 | 98.1490 | 78.6703 | 14548 | 2427 | 14582 | 275 | 104 | 37.8182 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 13.1073 | 56.8627 | 7.4074 | 75.4950 | 29 | 22 | 22 | 275 | 2 | 0.7273 | |
| dgrover-gatk | INDEL | I6_15 | * | homalt | 97.7715 | 99.8557 | 95.7725 | 55.4177 | 6230 | 9 | 6230 | 275 | 272 | 98.9091 | |