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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
9901-9950 / 86044 show all | |||||||||||||||
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3353 | 99.0372 | 99.6352 | 71.5761 | 32916 | 320 | 32773 | 120 | 43 | 35.8333 | |
| gduggal-bwaplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 59.5931 | 46.9320 | 81.6092 | 83.6389 | 283 | 320 | 284 | 64 | 1 | 1.5625 | |
| gduggal-snapplat | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 87.6253 | 90.1478 | 85.2402 | 88.4281 | 2928 | 320 | 2928 | 507 | 25 | 4.9310 | |
| gduggal-snapplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 51.0719 | 55.5556 | 47.2579 | 93.7840 | 400 | 320 | 405 | 452 | 26 | 5.7522 | |
| gduggal-snapvard | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 0.0000 | 65.3304 | 0.0000 | 0.0000 | 603 | 320 | 0 | 0 | 0 | ||
| ghariani-varprowl | SNP | ti | map_l150_m2_e1 | * | 97.8866 | 98.4558 | 97.3240 | 80.2448 | 20403 | 320 | 20403 | 561 | 134 | 23.8859 | |
| gduggal-snapvard | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 97.9882 | 96.8323 | 99.1721 | 49.4419 | 9782 | 320 | 9703 | 81 | 32 | 39.5062 | |
| bgallagher-sentieon | SNP | * | map_l100_m2_e0 | * | 99.4275 | 99.5674 | 99.2880 | 67.0766 | 73644 | 320 | 73633 | 528 | 81 | 15.3409 | |
| bgallagher-sentieon | SNP | * | map_siren | het | 99.4455 | 99.6483 | 99.2436 | 58.2943 | 90671 | 320 | 90657 | 691 | 77 | 11.1433 | |
| ckim-vqsr | SNP | tv | map_l250_m0_e0 | het | 60.2871 | 44.0559 | 95.4545 | 98.5526 | 252 | 320 | 252 | 12 | 0 | 0.0000 | |
| ckim-isaac | INDEL | D16_PLUS | * | homalt | 88.9191 | 81.0875 | 98.4252 | 54.0612 | 1372 | 320 | 1375 | 22 | 6 | 27.2727 | |
| ltrigg-rtg1 | SNP | ti | map_l125_m0_e0 | * | 98.6208 | 97.4926 | 99.7755 | 64.1831 | 12442 | 320 | 12442 | 28 | 12 | 42.8571 | |
| jpowers-varprowl | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.8917 | 98.2074 | 97.5780 | 64.8285 | 17531 | 320 | 17606 | 437 | 24 | 5.4920 | |
| gduggal-bwaplat | INDEL | D1_5 | map_l100_m2_e0 | het | 84.9116 | 74.6019 | 98.5279 | 92.8459 | 937 | 319 | 937 | 14 | 5 | 35.7143 | |
| gduggal-bwaplat | INDEL | D1_5 | map_l150_m2_e1 | * | 73.9130 | 58.9974 | 98.9224 | 95.6603 | 459 | 319 | 459 | 5 | 1 | 20.0000 | |
| gduggal-bwafb | INDEL | D6_15 | HG002complexvar | het | 93.9461 | 89.7756 | 98.5230 | 50.1907 | 2801 | 319 | 3602 | 54 | 30 | 55.5556 | |
| gduggal-bwafb | SNP | ti | HG002complexvar | homalt | 99.8904 | 99.8351 | 99.9457 | 18.2578 | 193145 | 319 | 193159 | 105 | 88 | 83.8095 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.7060 | 96.2006 | 99.2594 | 58.4607 | 8077 | 319 | 8041 | 60 | 42 | 70.0000 | |
| rpoplin-dv42 | INDEL | I16_PLUS | * | hetalt | 91.5838 | 84.7950 | 99.5541 | 49.0051 | 1779 | 319 | 1786 | 8 | 7 | 87.5000 | |
| cchapple-custom | SNP | tv | map_l100_m0_e0 | * | 96.3944 | 97.1220 | 95.6777 | 73.2738 | 10765 | 319 | 10758 | 486 | 83 | 17.0782 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 91.8646 | 89.3667 | 94.5063 | 68.0289 | 2681 | 319 | 2632 | 153 | 61 | 39.8693 | |
| ckim-isaac | INDEL | * | map_l125_m2_e0 | homalt | 73.3884 | 58.1913 | 99.3289 | 81.2185 | 444 | 319 | 444 | 3 | 1 | 33.3333 | |
| ciseli-custom | INDEL | D1_5 | map_l125_m2_e1 | * | 76.9744 | 72.4287 | 82.1289 | 90.9356 | 838 | 319 | 841 | 183 | 83 | 45.3552 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | * | het | 93.4104 | 88.2634 | 99.1949 | 47.8107 | 2399 | 319 | 2341 | 19 | 7 | 36.8421 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 85.9409 | 75.3478 | 100.0000 | 40.3027 | 975 | 319 | 1065 | 0 | 0 | ||
| qzeng-custom | SNP | * | segdup | * | 98.6778 | 98.8634 | 98.4928 | 92.2719 | 27748 | 319 | 27512 | 421 | 68 | 16.1520 | |
| ndellapenna-hhga | INDEL | D16_PLUS | HG002complexvar | * | 84.9902 | 80.5843 | 89.9058 | 63.0348 | 1324 | 319 | 1336 | 150 | 106 | 70.6667 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.2939 | 98.0121 | 98.5773 | 60.5225 | 15728 | 319 | 15729 | 227 | 215 | 94.7137 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.0207 | 95.3171 | 98.7864 | 34.4210 | 6493 | 319 | 6512 | 80 | 77 | 96.2500 | |
| anovak-vg | INDEL | * | map_l100_m0_e0 | het | 71.5575 | 68.7561 | 74.5968 | 89.0375 | 702 | 319 | 740 | 252 | 75 | 29.7619 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.3908 | 95.3819 | 99.4860 | 25.9321 | 6568 | 318 | 6581 | 34 | 33 | 97.0588 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.9885 | 94.6447 | 99.4513 | 62.5582 | 5620 | 318 | 6163 | 34 | 32 | 94.1176 | |
| astatham-gatk | INDEL | * | HG002complexvar | het | 99.5588 | 99.3119 | 99.8070 | 57.7885 | 45894 | 318 | 45516 | 88 | 55 | 62.5000 | |
| ciseli-custom | INDEL | D1_5 | map_l100_m2_e1 | het | 79.5099 | 74.9211 | 84.6975 | 89.9093 | 950 | 318 | 952 | 172 | 40 | 23.2558 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.6291 | 95.3819 | 99.9848 | 25.9951 | 6568 | 318 | 6581 | 1 | 0 | 0.0000 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.5858 | 97.9822 | 99.1968 | 53.1729 | 15442 | 318 | 15438 | 125 | 48 | 38.4000 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 92.1673 | 95.3799 | 89.1641 | 87.4464 | 6565 | 318 | 6443 | 783 | 169 | 21.5837 | |
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 12.5922 | 6.7449 | 94.6237 | 51.3089 | 23 | 318 | 88 | 5 | 5 | 100.0000 | |
| rpoplin-dv42 | INDEL | I16_PLUS | HG002compoundhet | hetalt | 91.7314 | 84.8065 | 99.8878 | 40.3479 | 1775 | 318 | 1781 | 2 | 2 | 100.0000 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 94.4711 | 89.8077 | 99.6454 | 42.6596 | 2802 | 318 | 2810 | 10 | 9 | 90.0000 | |
| dgrover-gatk | SNP | * | map_l125_m2_e0 | * | 99.3279 | 99.3194 | 99.3363 | 74.2156 | 46405 | 318 | 46399 | 310 | 69 | 22.2581 | |
| dgrover-gatk | SNP | * | map_l125_m2_e1 | * | 99.3336 | 99.3263 | 99.3409 | 74.2508 | 46884 | 318 | 46878 | 311 | 69 | 22.1865 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 81.0289 | 75.8175 | 87.0096 | 52.5248 | 997 | 318 | 998 | 149 | 131 | 87.9195 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 43.5045 | 31.1688 | 72.0000 | 59.1837 | 144 | 318 | 144 | 56 | 49 | 87.5000 | |
| ghariani-varprowl | SNP | ti | map_l150_m2_e0 | * | 97.8795 | 98.4497 | 97.3158 | 80.1688 | 20194 | 318 | 20194 | 557 | 133 | 23.8779 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 65.0860 | 56.7347 | 76.3203 | 57.3091 | 417 | 318 | 448 | 139 | 119 | 85.6115 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 90.3706 | 96.6600 | 84.8496 | 55.8282 | 9203 | 318 | 9196 | 1642 | 1614 | 98.2948 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 93.6959 | 90.9221 | 96.6443 | 51.2348 | 3175 | 317 | 3168 | 110 | 81 | 73.6364 | |
| jlack-gatk | SNP | * | map_l125_m0_e0 | * | 94.5944 | 98.3647 | 91.1024 | 82.9942 | 19068 | 317 | 19065 | 1862 | 148 | 7.9484 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.7838 | 96.2244 | 99.3945 | 58.5102 | 8079 | 317 | 8044 | 49 | 40 | 81.6327 | |