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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
12001-12050 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 91.5880 | 92.9697 | 90.2468 | 68.7592 | 767 | 58 | 768 | 83 | 69 | 83.1325 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 93.4664 | 90.7546 | 96.3452 | 62.2067 | 2189 | 223 | 2188 | 83 | 56 | 67.4699 | |
| qzeng-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 94.7018 | 96.2862 | 93.1687 | 88.3587 | 1063 | 41 | 1132 | 83 | 31 | 37.3494 | |
| qzeng-custom | INDEL | I1_5 | map_l100_m1_e0 | * | 81.6840 | 71.9940 | 94.3881 | 86.6528 | 964 | 375 | 1396 | 83 | 16 | 19.2771 | |
| qzeng-custom | INDEL | I1_5 | map_siren | het | 87.6104 | 81.4396 | 94.7930 | 85.2134 | 1369 | 312 | 1511 | 83 | 20 | 24.0964 | |
| ltrigg-rtg2 | SNP | ti | map_l100_m2_e0 | * | 99.2429 | 98.6642 | 99.8285 | 55.8705 | 48307 | 654 | 48309 | 83 | 19 | 22.8916 | |
| mlin-fermikit | INDEL | * | map_l125_m0_e0 | homalt | 64.5756 | 61.6197 | 67.8295 | 81.8820 | 175 | 109 | 175 | 83 | 68 | 81.9277 | |
| ndellapenna-hhga | INDEL | * | HG002complexvar | hetalt | 86.5340 | 77.9941 | 97.1740 | 71.6888 | 2885 | 814 | 2854 | 83 | 75 | 90.3614 | |
| gduggal-snapvard | SNP | tv | segdup | het | 97.6892 | 96.9926 | 98.3958 | 95.3896 | 5128 | 159 | 5091 | 83 | 12 | 14.4578 | |
| gduggal-snapvard | INDEL | D6_15 | map_l100_m2_e1 | * | 65.5947 | 59.6364 | 72.8758 | 83.1683 | 164 | 111 | 223 | 83 | 59 | 71.0843 | |
| ghariani-varprowl | INDEL | I1_5 | map_l100_m2_e0 | het | 94.1968 | 98.3607 | 90.3712 | 90.4265 | 780 | 13 | 779 | 83 | 29 | 34.9398 | |
| gduggal-snapvard | INDEL | C1_5 | map_l100_m2_e0 | * | 0.0000 | 0.0000 | 48.7654 | 95.6463 | 0 | 0 | 79 | 83 | 9 | 10.8434 | |
| gduggal-snapfb | SNP | * | map_l100_m2_e0 | homalt | 98.4327 | 97.2060 | 99.6907 | 70.5354 | 26754 | 769 | 26756 | 83 | 30 | 36.1446 | |
| gduggal-snapfb | SNP | * | map_l100_m2_e1 | homalt | 98.4483 | 97.2334 | 99.6939 | 70.5179 | 27027 | 769 | 27029 | 83 | 30 | 36.1446 | |
| anovak-vg | INDEL | I1_5 | map_l150_m1_e0 | het | 51.0679 | 42.8094 | 63.2743 | 93.1411 | 128 | 171 | 143 | 83 | 7 | 8.4337 | |
| bgallagher-sentieon | SNP | ti | map_l250_m2_e0 | * | 98.6664 | 98.9816 | 98.3532 | 89.5470 | 4957 | 51 | 4957 | 83 | 19 | 22.8916 | |
| astatham-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5109 | 97.3461 | 99.7039 | 72.1148 | 27950 | 762 | 27950 | 83 | 24 | 28.9157 | |
| astatham-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.5109 | 97.3461 | 99.7039 | 72.1148 | 27950 | 762 | 27950 | 83 | 24 | 28.9157 | |
| astatham-gatk | SNP | * | map_l150_m1_e0 | * | 91.4460 | 84.4686 | 99.6799 | 78.7872 | 25855 | 4754 | 25849 | 83 | 39 | 46.9880 | |
| asubramanian-gatk | INDEL | C1_5 | HG002compoundhet | het | 0.0000 | 0.0000 | 51.4620 | 0 | 0 | 0 | 83 | 0 | 0.0000 | ||
| asubramanian-gatk | INDEL | D6_15 | HG002complexvar | * | 97.5846 | 96.7748 | 98.4081 | 58.8477 | 5131 | 171 | 5131 | 83 | 77 | 92.7711 | |
| asubramanian-gatk | INDEL | I6_15 | * | het | 98.1049 | 97.0796 | 99.1521 | 59.9730 | 9740 | 293 | 9706 | 83 | 53 | 63.8554 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 9.3220 | 7.7465 | 11.7021 | 43.7126 | 11 | 131 | 11 | 83 | 83 | 100.0000 | |
| jpowers-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | het | 17.0940 | 41.6667 | 10.7527 | 42.2360 | 10 | 14 | 10 | 83 | 83 | 100.0000 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.9259 | 94.5255 | 99.4514 | 70.4506 | 14573 | 844 | 15046 | 83 | 82 | 98.7952 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 92.7361 | 97.4125 | 88.4882 | 79.5170 | 640 | 17 | 638 | 83 | 78 | 93.9759 | |
| jli-custom | INDEL | D6_15 | HG002compoundhet | het | 93.6150 | 96.6121 | 90.7982 | 65.4935 | 827 | 29 | 819 | 83 | 81 | 97.5904 | |
| jli-custom | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.5868 | 99.9441 | 99.2321 | 39.7088 | 10726 | 6 | 10726 | 83 | 1 | 1.2048 | |
| jli-custom | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.3587 | 99.9407 | 98.7835 | 42.3002 | 6740 | 4 | 6740 | 83 | 1 | 1.2048 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 84.3015 | 79.4055 | 89.8409 | 68.3211 | 748 | 194 | 734 | 83 | 52 | 62.6506 | |
| ckim-vqsr | INDEL | * | map_l100_m2_e0 | * | 97.1833 | 96.6423 | 97.7304 | 89.4395 | 3569 | 124 | 3574 | 83 | 16 | 19.2771 | |
| ckim-vqsr | INDEL | * | map_l100_m2_e1 | * | 97.1482 | 96.5389 | 97.7652 | 89.4752 | 3626 | 130 | 3631 | 83 | 16 | 19.2771 | |
| ckim-vqsr | SNP | ti | segdup | het | 98.9319 | 98.5619 | 99.3047 | 94.5420 | 11857 | 173 | 11855 | 83 | 4 | 4.8193 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.0142 | 90.8795 | 95.2517 | 63.6364 | 1674 | 168 | 1665 | 83 | 41 | 49.3976 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.0024 | 96.5790 | 99.4683 | 68.2096 | 15527 | 550 | 15528 | 83 | 69 | 83.1325 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.0024 | 96.5790 | 99.4683 | 68.2096 | 15527 | 550 | 15528 | 83 | 69 | 83.1325 | |
| raldana-dualsentieon | INDEL | D16_PLUS | HG002compoundhet | het | 81.9000 | 89.8765 | 75.2239 | 57.3791 | 364 | 41 | 252 | 83 | 82 | 98.7952 | |
| rpoplin-dv42 | INDEL | I1_5 | * | homalt | 99.6318 | 99.4026 | 99.8620 | 52.4571 | 60067 | 361 | 60064 | 83 | 77 | 92.7711 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.7863 | 96.9500 | 96.6233 | 75.9515 | 2384 | 75 | 2375 | 83 | 74 | 89.1566 | |
| rpoplin-dv42 | SNP | tv | map_l125_m0_e0 | het | 98.3333 | 98.5458 | 98.1217 | 74.3380 | 4337 | 64 | 4336 | 83 | 43 | 51.8072 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | het | 59.9292 | 69.6296 | 52.6012 | 68.2569 | 94 | 41 | 91 | 82 | 79 | 96.3415 | |
| raldana-dualsentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 94.0384 | 95.2632 | 92.8447 | 81.0891 | 1267 | 63 | 1064 | 82 | 76 | 92.6829 | |
| raldana-dualsentieon | INDEL | I16_PLUS | HG002compoundhet | * | 92.4081 | 89.1741 | 95.8856 | 50.9476 | 1911 | 232 | 1911 | 82 | 81 | 98.7805 | |
| gduggal-snapfb | SNP | * | map_l100_m1_e0 | homalt | 98.4097 | 97.1633 | 99.6885 | 68.9633 | 26237 | 766 | 26239 | 82 | 29 | 35.3659 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 70.5199 | 59.6244 | 86.2876 | 93.0181 | 508 | 344 | 516 | 82 | 38 | 46.3415 | |
| gduggal-snapvard | INDEL | C1_5 | map_l100_m2_e0 | het | 0.0000 | 0.0000 | 41.0072 | 95.7686 | 0 | 0 | 57 | 82 | 9 | 10.9756 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 8.2305 | 5.2083 | 19.6078 | 88.3429 | 20 | 364 | 20 | 82 | 46 | 56.0976 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 12.5828 | 9.4527 | 18.8119 | 88.2558 | 19 | 182 | 19 | 82 | 46 | 56.0976 | |
| gduggal-snapvard | INDEL | D6_15 | map_l100_m2_e0 | * | 66.9120 | 61.7424 | 73.0263 | 82.9213 | 163 | 101 | 222 | 82 | 58 | 70.7317 | |
| gduggal-snapvard | INDEL | I1_5 | map_l125_m0_e0 | het | 87.9923 | 98.4375 | 79.5511 | 91.6753 | 189 | 3 | 319 | 82 | 26 | 31.7073 | |