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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
16251-16300 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.3814 | 98.9733 | 99.7930 | 65.0253 | 482 | 5 | 482 | 1 | 1 | 100.0000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0126 | 98.9729 | 99.0524 | 59.2954 | 19658 | 204 | 19651 | 188 | 96 | 51.0638 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.1117 | 98.9729 | 99.2509 | 77.5593 | 1349 | 14 | 1325 | 10 | 5 | 50.0000 | |
| rpoplin-dv42 | SNP | tv | map_l125_m1_e0 | het | 98.9777 | 98.9729 | 98.9825 | 69.6562 | 10022 | 104 | 10020 | 103 | 54 | 52.4272 | |
| astatham-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.2975 | 98.9729 | 99.6243 | 77.9307 | 1349 | 14 | 1326 | 5 | 3 | 60.0000 | |
| ckim-gatk | SNP | tv | HG002compoundhet | het | 99.2595 | 98.9728 | 99.5478 | 55.8932 | 4625 | 48 | 4623 | 21 | 13 | 61.9048 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.7631 | 98.9728 | 98.5542 | 60.1632 | 1638 | 17 | 1636 | 24 | 21 | 87.5000 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.3981 | 98.9726 | 99.8273 | 17.0487 | 578 | 6 | 578 | 1 | 1 | 100.0000 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 94.6615 | 98.9726 | 90.7104 | 82.2631 | 867 | 9 | 664 | 68 | 63 | 92.6471 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 94.4810 | 98.9726 | 90.3794 | 82.0961 | 867 | 9 | 667 | 71 | 69 | 97.1831 | |
| jlack-gatk | INDEL | D1_5 | map_siren | homalt | 99.3983 | 98.9726 | 99.8277 | 79.2900 | 1156 | 12 | 1159 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.4836 | 98.9726 | 100.0000 | 18.6798 | 578 | 6 | 579 | 0 | 0 | ||
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 95.0745 | 98.9726 | 91.4718 | 82.4269 | 867 | 9 | 665 | 62 | 60 | 96.7742 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.4836 | 98.9726 | 100.0000 | 18.6798 | 578 | 6 | 579 | 0 | 0 | ||
| ltrigg-rtg2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.3201 | 98.9723 | 99.6702 | 83.1011 | 1252 | 13 | 1209 | 4 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | D1_5 | map_l150_m2_e1 | * | 97.9683 | 98.9717 | 96.9849 | 89.2621 | 770 | 8 | 772 | 24 | 4 | 16.6667 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l150_m2_e1 | * | 98.2175 | 98.9717 | 97.4747 | 89.6498 | 770 | 8 | 772 | 20 | 5 | 25.0000 | |
| gduggal-snapvard | SNP | * | * | het | 98.8907 | 98.9717 | 98.8098 | 27.4520 | 1854334 | 19266 | 1842523 | 22194 | 3216 | 14.4904 | |
| cchapple-custom | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.1597 | 98.9715 | 99.3486 | 67.2313 | 4715 | 49 | 4728 | 31 | 4 | 12.9032 | |
| egarrison-hhga | SNP | ti | map_l100_m1_e0 | het | 99.3929 | 98.9713 | 99.8181 | 63.9434 | 29634 | 308 | 29635 | 54 | 18 | 33.3333 | |
| ckim-dragen | SNP | * | map_l125_m2_e1 | het | 97.7443 | 98.9710 | 96.5476 | 78.6185 | 29335 | 305 | 29336 | 1049 | 91 | 8.6749 | |
| jli-custom | SNP | ti | map_l250_m2_e0 | homalt | 99.4256 | 98.9708 | 99.8846 | 85.5643 | 1731 | 18 | 1731 | 2 | 2 | 100.0000 | |
| bgallagher-sentieon | SNP | ti | map_l250_m2_e0 | homalt | 99.3685 | 98.9708 | 99.7695 | 86.1400 | 1731 | 18 | 1731 | 4 | 3 | 75.0000 | |
| raldana-dualsentieon | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.3531 | 98.9700 | 99.7391 | 58.7473 | 55058 | 573 | 55048 | 144 | 22 | 15.2778 | |
| ghariani-varprowl | SNP | * | map_l125_m2_e0 | het | 97.3365 | 98.9699 | 95.7561 | 79.6531 | 29016 | 302 | 29016 | 1286 | 236 | 18.3515 | |
| ckim-dragen | SNP | * | map_l250_m2_e1 | homalt | 99.1340 | 98.9698 | 99.2986 | 84.0205 | 2690 | 28 | 2690 | 19 | 16 | 84.2105 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.3962 | 98.9698 | 99.8262 | 37.7685 | 4035 | 42 | 4020 | 7 | 2 | 28.5714 | |
| hfeng-pmm1 | SNP | ti | map_l150_m0_e0 | * | 99.1145 | 98.9696 | 99.2598 | 79.4196 | 7780 | 81 | 7778 | 58 | 12 | 20.6897 | |
| astatham-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.2248 | 98.9691 | 99.4819 | 76.0248 | 384 | 4 | 384 | 2 | 1 | 50.0000 | |
| ckim-dragen | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3532 | 98.9691 | 99.7403 | 76.7652 | 384 | 4 | 384 | 1 | 1 | 100.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | HG002compoundhet | homalt | 93.1153 | 98.9691 | 87.9154 | 78.3801 | 288 | 3 | 291 | 40 | 38 | 95.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.2248 | 98.9691 | 99.4819 | 76.1286 | 384 | 4 | 384 | 2 | 1 | 50.0000 | |
| jli-custom | INDEL | I1_5 | HG002complexvar | * | 99.4264 | 98.9689 | 99.8882 | 55.8919 | 33019 | 344 | 33052 | 37 | 27 | 72.9730 | |
| gduggal-bwafb | SNP | * | map_l150_m2_e1 | homalt | 99.4055 | 98.9685 | 99.8465 | 74.9037 | 11705 | 122 | 11705 | 18 | 11 | 61.1111 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3204 | 98.9679 | 99.6754 | 59.9358 | 19657 | 205 | 19650 | 64 | 45 | 70.3125 | |
| rpoplin-dv42 | SNP | ti | map_l125_m2_e1 | het | 99.1705 | 98.9679 | 99.3738 | 71.8144 | 18890 | 197 | 18886 | 119 | 74 | 62.1849 | |
| ltrigg-rtg1 | INDEL | * | HG002complexvar | homalt | 99.4013 | 98.9677 | 99.8388 | 52.4987 | 26747 | 279 | 26629 | 43 | 32 | 74.4186 | |
| rpoplin-dv42 | SNP | ti | map_l125_m2_e0 | het | 99.1665 | 98.9669 | 99.3669 | 71.7774 | 18681 | 195 | 18677 | 119 | 74 | 62.1849 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 98.4958 | 98.9669 | 98.0290 | 61.4708 | 958 | 10 | 945 | 19 | 19 | 100.0000 | |
| astatham-gatk | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.4684 | 98.9668 | 99.9751 | 45.9140 | 4023 | 42 | 4023 | 1 | 0 | 0.0000 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.7763 | 98.9668 | 96.6142 | 83.7783 | 1341 | 14 | 1227 | 43 | 16 | 37.2093 | |
| astatham-gatk | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.4603 | 98.9667 | 99.9588 | 33.4796 | 7279 | 76 | 7275 | 3 | 2 | 66.6667 | |
| rpoplin-dv42 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.7353 | 98.9667 | 98.5050 | 75.1773 | 2969 | 31 | 2965 | 45 | 33 | 73.3333 | |
| ckim-dragen | SNP | * | map_l125_m2_e0 | het | 97.7348 | 98.9665 | 96.5334 | 78.5462 | 29015 | 303 | 29016 | 1042 | 91 | 8.7332 | |
| rpoplin-dv42 | INDEL | * | map_l125_m2_e1 | homalt | 99.0304 | 98.9664 | 99.0944 | 86.2407 | 766 | 8 | 766 | 7 | 6 | 85.7143 | |
| ndellapenna-hhga | INDEL | * | map_l125_m2_e1 | homalt | 98.9664 | 98.9664 | 98.9664 | 85.9247 | 766 | 8 | 766 | 8 | 6 | 75.0000 | |
| dgrover-gatk | INDEL | * | map_l125_m2_e1 | homalt | 98.9025 | 98.9664 | 98.8387 | 87.1943 | 766 | 8 | 766 | 9 | 4 | 44.4444 | |
| gduggal-snapvard | SNP | ti | * | homalt | 99.4493 | 98.9663 | 99.9370 | 16.0694 | 794738 | 8301 | 790421 | 498 | 326 | 65.4618 | |
| gduggal-bwafb | SNP | * | map_l150_m2_e0 | homalt | 99.4033 | 98.9657 | 99.8448 | 74.8531 | 11578 | 121 | 11578 | 18 | 11 | 61.1111 | |
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.6853 | 98.9657 | 98.4065 | 63.1662 | 15597 | 163 | 15439 | 250 | 223 | 89.2000 | |