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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
40951-41000 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 88.0509 | 79.0340 | 99.3902 | 32.6949 | 1440 | 382 | 1467 | 9 | 8 | 88.8889 | |
| raldana-dualsentieon | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 87.8883 | 79.0323 | 98.9796 | 99.9286 | 98 | 26 | 97 | 1 | 0 | 0.0000 | |
| jpowers-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 66.1090 | 79.0323 | 56.8182 | 83.1418 | 49 | 13 | 50 | 38 | 38 | 100.0000 | |
| ckim-isaac | INDEL | * | * | hetalt | 87.6357 | 79.0308 | 98.3434 | 43.3219 | 19945 | 5292 | 20303 | 342 | 304 | 88.8889 | |
| qzeng-custom | INDEL | * | map_l100_m1_e0 | * | 83.9800 | 79.0296 | 89.5920 | 87.4621 | 2834 | 752 | 3667 | 426 | 66 | 15.4930 | |
| qzeng-custom | INDEL | D1_5 | map_l100_m0_e0 | * | 86.8238 | 79.0267 | 96.3280 | 91.0593 | 682 | 181 | 787 | 30 | 23 | 76.6667 | |
| asubramanian-gatk | INDEL | I1_5 | map_l100_m1_e0 | het | 87.1648 | 79.0219 | 97.1787 | 89.3631 | 614 | 163 | 620 | 18 | 2 | 11.1111 | |
| jpowers-varprowl | INDEL | I6_15 | map_siren | het | 74.0667 | 79.0210 | 69.6970 | 82.9193 | 113 | 30 | 115 | 50 | 50 | 100.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | map_siren | * | 81.2950 | 79.0210 | 83.7037 | 88.3520 | 113 | 30 | 113 | 22 | 15 | 68.1818 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 84.9493 | 79.0158 | 91.8463 | 60.4412 | 3950 | 1049 | 3920 | 348 | 245 | 70.4023 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 84.9493 | 79.0158 | 91.8463 | 60.4412 | 3950 | 1049 | 3920 | 348 | 245 | 70.4023 | |
| ckim-isaac | INDEL | * | HG002compoundhet | * | 82.5676 | 79.0154 | 86.4543 | 46.0363 | 23673 | 6287 | 22964 | 3598 | 3236 | 89.9389 | |
| ciseli-custom | INDEL | * | HG002compoundhet | homalt | 5.5419 | 79.0087 | 2.8717 | 55.4798 | 542 | 144 | 559 | 18907 | 17855 | 94.4359 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 74.5876 | 79.0062 | 70.6370 | 92.2018 | 5438 | 1445 | 5456 | 2268 | 88 | 3.8801 | |
| ciseli-custom | SNP | tv | map_l100_m1_e0 | * | 82.8010 | 79.0049 | 86.9802 | 71.6783 | 19357 | 5144 | 19347 | 2896 | 701 | 24.2058 | |
| gduggal-bwavard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 88.0582 | 79.0032 | 99.4576 | 57.3453 | 1490 | 396 | 1467 | 8 | 7 | 87.5000 | |
| gduggal-snapplat | INDEL | I1_5 | map_l125_m2_e0 | * | 84.1285 | 78.9965 | 89.9736 | 93.9438 | 677 | 180 | 682 | 76 | 4 | 5.2632 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 87.7042 | 78.9949 | 98.5719 | 61.4567 | 2971 | 790 | 2968 | 43 | 28 | 65.1163 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 87.7042 | 78.9949 | 98.5719 | 61.4567 | 2971 | 790 | 2968 | 43 | 28 | 65.1163 | |
| anovak-vg | SNP | * | map_l100_m0_e0 | homalt | 87.9850 | 78.9931 | 99.2870 | 62.5031 | 9179 | 2441 | 9052 | 65 | 58 | 89.2308 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 31.6999 | 78.9855 | 19.8291 | 89.3462 | 218 | 58 | 232 | 938 | 21 | 2.2388 | |
| hfeng-pmm2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 86.8589 | 78.9855 | 96.4758 | 90.1732 | 218 | 58 | 219 | 8 | 0 | 0.0000 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 74.7354 | 78.9833 | 70.9211 | 58.2978 | 1041 | 277 | 1178 | 483 | 222 | 45.9627 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 85.6343 | 78.9796 | 93.5135 | 45.7111 | 387 | 103 | 2249 | 156 | 148 | 94.8718 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 81.8009 | 78.9787 | 84.8322 | 50.9671 | 11677 | 3108 | 11678 | 2088 | 2070 | 99.1379 | |
| gduggal-bwaplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 87.4697 | 78.9719 | 98.0167 | 90.7130 | 11507 | 3064 | 11515 | 233 | 49 | 21.0300 | |
| gduggal-bwaplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 87.4697 | 78.9719 | 98.0167 | 90.7130 | 11507 | 3064 | 11515 | 233 | 49 | 21.0300 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 70.7753 | 78.9709 | 64.1209 | 53.4898 | 4420 | 1177 | 8614 | 4820 | 4189 | 86.9087 | |
| gduggal-bwaplat | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 87.9523 | 78.9685 | 99.2424 | 47.1530 | 1179 | 314 | 1179 | 9 | 9 | 100.0000 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 88.2006 | 78.9671 | 99.8794 | 42.7486 | 841 | 224 | 828 | 1 | 1 | 100.0000 | |
| qzeng-custom | SNP | * | map_l100_m2_e1 | homalt | 87.9899 | 78.9574 | 99.3560 | 60.6459 | 21947 | 5849 | 21600 | 140 | 134 | 95.7143 | |
| qzeng-custom | INDEL | I1_5 | map_l125_m2_e0 | hetalt | 88.2353 | 78.9474 | 100.0000 | 91.7160 | 15 | 4 | 14 | 0 | 0 | ||
| qzeng-custom | INDEL | I1_5 | map_l125_m2_e1 | hetalt | 88.2353 | 78.9474 | 100.0000 | 91.8605 | 15 | 4 | 14 | 0 | 0 | ||
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 88.2353 | 78.9474 | 100.0000 | 70.9677 | 15 | 4 | 18 | 0 | 0 | ||
| rpoplin-dv42 | INDEL | D16_PLUS | map_l100_m0_e0 | het | 88.2353 | 78.9474 | 100.0000 | 93.3921 | 15 | 4 | 15 | 0 | 0 | ||
| gduggal-bwavard | INDEL | I16_PLUS | segdup | homalt | 88.2353 | 78.9474 | 100.0000 | 86.8421 | 15 | 4 | 15 | 0 | 0 | ||
| gduggal-bwavard | INDEL | D16_PLUS | map_l100_m0_e0 | het | 50.8475 | 78.9474 | 37.5000 | 94.1349 | 15 | 4 | 15 | 25 | 4 | 16.0000 | |
| anovak-vg | INDEL | D1_5 | tech_badpromoters | * | 88.2353 | 78.9474 | 100.0000 | 40.0000 | 15 | 4 | 15 | 0 | 0 | ||
| asubramanian-gatk | INDEL | D16_PLUS | map_l100_m0_e0 | het | 78.3582 | 78.9474 | 77.7778 | 97.5577 | 15 | 4 | 14 | 4 | 0 | 0.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 84.9057 | 78.9474 | 91.8367 | 99.3649 | 45 | 12 | 45 | 4 | 0 | 0.0000 | |
| ckim-isaac | INDEL | D6_15 | map_l125_m1_e0 | hetalt | 85.7143 | 78.9474 | 93.7500 | 80.0000 | 15 | 4 | 15 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | D6_15 | map_l125_m2_e0 | hetalt | 85.7143 | 78.9474 | 93.7500 | 82.2222 | 15 | 4 | 15 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 83.7989 | 78.9474 | 89.2857 | 81.8182 | 15 | 4 | 25 | 3 | 3 | 100.0000 | |
| ciseli-custom | INDEL | I1_5 | map_siren | het | 73.5105 | 78.9411 | 68.7790 | 81.4258 | 1327 | 354 | 1335 | 606 | 517 | 85.3135 | |
| gduggal-snapplat | INDEL | I1_5 | map_l125_m2_e1 | het | 82.6084 | 78.9370 | 86.6379 | 94.9067 | 401 | 107 | 402 | 62 | 3 | 4.8387 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 85.7237 | 78.9364 | 93.7881 | 67.9922 | 757 | 202 | 770 | 51 | 38 | 74.5098 | |
| ckim-isaac | INDEL | I6_15 | * | * | 86.2978 | 78.9268 | 95.1875 | 41.9911 | 19592 | 5231 | 19601 | 991 | 727 | 73.3602 | |
| qzeng-custom | INDEL | D1_5 | map_l125_m2_e0 | het | 86.7233 | 78.9267 | 96.2291 | 92.7251 | 603 | 161 | 689 | 27 | 21 | 77.7778 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 83.6293 | 78.9187 | 88.9381 | 47.0175 | 3766 | 1006 | 1809 | 225 | 103 | 45.7778 | |
| qzeng-custom | SNP | ti | map_l100_m2_e0 | homalt | 87.9965 | 78.9175 | 99.4361 | 59.4553 | 14449 | 3860 | 14284 | 81 | 75 | 92.5926 | |