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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
70201-70250 / 86044 show all | |||||||||||||||
| ghariani-varprowl | INDEL | * | func_cds | * | 91.6388 | 92.3596 | 90.9292 | 61.0680 | 411 | 34 | 411 | 41 | 30 | 73.1707 | |
| ghariani-varprowl | INDEL | D1_5 | map_l250_m1_e0 | * | 86.3271 | 94.1520 | 79.7030 | 96.1626 | 161 | 10 | 161 | 41 | 4 | 9.7561 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 29.7662 | 18.0480 | 84.8708 | 63.2791 | 233 | 1058 | 230 | 41 | 31 | 75.6098 | |
| gduggal-snapplat | INDEL | I1_5 | func_cds | * | 72.3894 | 69.4444 | 75.5952 | 55.4377 | 125 | 55 | 127 | 41 | 1 | 2.4390 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 55.2595 | 38.9041 | 95.3409 | 37.9408 | 852 | 1338 | 839 | 41 | 31 | 75.6098 | |
| gduggal-snapplat | INDEL | * | map_l100_m1_e0 | homalt | 84.8014 | 75.8761 | 96.1064 | 87.1554 | 931 | 296 | 1012 | 41 | 2 | 4.8781 | |
| gduggal-snapplat | INDEL | * | map_l100_m2_e0 | homalt | 84.9002 | 75.9715 | 96.2072 | 87.8170 | 958 | 303 | 1040 | 41 | 2 | 4.8781 | |
| gduggal-snapplat | INDEL | * | map_l100_m2_e1 | homalt | 84.9123 | 75.9563 | 96.2625 | 87.8918 | 973 | 308 | 1056 | 41 | 2 | 4.8781 | |
| hfeng-pmm1 | INDEL | * | map_siren | het | 98.4945 | 97.9148 | 99.0811 | 80.4769 | 4414 | 94 | 4421 | 41 | 3 | 7.3171 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.4907 | 96.3100 | 96.6721 | 79.6867 | 1305 | 50 | 1191 | 41 | 29 | 70.7317 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 75.8784 | 82.4324 | 70.2899 | 72.7811 | 122 | 26 | 97 | 41 | 41 | 100.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.3350 | 98.3733 | 98.2966 | 76.2904 | 2419 | 40 | 2366 | 41 | 27 | 65.8537 | |
| jlack-gatk | INDEL | I1_5 | map_l150_m2_e1 | * | 95.3476 | 98.1168 | 92.7305 | 92.6905 | 521 | 10 | 523 | 41 | 4 | 9.7561 | |
| jlack-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.0016 | 98.8665 | 99.1370 | 66.6503 | 4710 | 54 | 4710 | 41 | 9 | 21.9512 | |
| hfeng-pmm3 | SNP | ti | map_l250_m1_e0 | * | 99.0936 | 99.0828 | 99.1044 | 88.3618 | 4537 | 42 | 4537 | 41 | 5 | 12.1951 | |
| hfeng-pmm3 | SNP | ti | map_l250_m2_e0 | * | 99.1712 | 99.1613 | 99.1811 | 88.8122 | 4966 | 42 | 4966 | 41 | 5 | 12.1951 | |
| hfeng-pmm3 | SNP | ti | map_l250_m2_e1 | * | 99.1724 | 99.1529 | 99.1920 | 88.8826 | 5033 | 43 | 5033 | 41 | 5 | 12.1951 | |
| hfeng-pmm3 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.0431 | 98.3803 | 99.7148 | 74.9713 | 14335 | 236 | 14335 | 41 | 7 | 17.0732 | |
| hfeng-pmm3 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.0431 | 98.3803 | 99.7148 | 74.9713 | 14335 | 236 | 14335 | 41 | 7 | 17.0732 | |
| hfeng-pmm1 | SNP | * | map_l250_m0_e0 | * | 98.1512 | 98.2201 | 98.0823 | 92.9304 | 2097 | 38 | 2097 | 41 | 9 | 21.9512 | |
| hfeng-pmm1 | SNP | tv | HG002complexvar | * | 99.8458 | 99.7087 | 99.9833 | 21.6860 | 245435 | 717 | 245349 | 41 | 20 | 48.7805 | |
| raldana-dualsentieon | SNP | tv | map_l250_m2_e0 | * | 98.1178 | 97.6752 | 98.5644 | 88.1773 | 2815 | 67 | 2815 | 41 | 3 | 7.3171 | |
| rpoplin-dv42 | INDEL | * | map_l100_m1_e0 | het | 97.7103 | 97.2707 | 98.1540 | 83.4501 | 2174 | 61 | 2180 | 41 | 18 | 43.9024 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.9414 | 98.3852 | 99.5039 | 60.3844 | 8225 | 135 | 8224 | 41 | 36 | 87.8049 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.9414 | 98.3852 | 99.5039 | 60.3844 | 8225 | 135 | 8224 | 41 | 36 | 87.8049 | |
| rpoplin-dv42 | SNP | tv | HG002complexvar | homalt | 99.9385 | 99.9201 | 99.9569 | 22.8530 | 95035 | 76 | 95011 | 41 | 37 | 90.2439 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.6617 | 94.2604 | 99.1884 | 62.0692 | 5009 | 305 | 5011 | 41 | 34 | 82.9268 | |
| raldana-dualsentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.2891 | 92.0962 | 98.7113 | 50.7555 | 3216 | 276 | 3217 | 42 | 36 | 85.7143 | |
| raldana-dualsentieon | SNP | tv | HG002complexvar | het | 99.7643 | 99.5575 | 99.9720 | 20.9789 | 150064 | 667 | 149985 | 42 | 9 | 21.4286 | |
| raldana-dualsentieon | SNP | tv | map_l250_m2_e1 | * | 98.1230 | 97.7023 | 98.5472 | 88.2575 | 2849 | 67 | 2849 | 42 | 3 | 7.1429 | |
| rpoplin-dv42 | SNP | tv | map_l250_m1_e0 | het | 97.6497 | 97.6497 | 97.6497 | 86.6731 | 1745 | 42 | 1745 | 42 | 26 | 61.9048 | |
| rpoplin-dv42 | INDEL | I6_15 | * | hetalt | 94.8036 | 90.5625 | 99.4614 | 37.3252 | 7744 | 807 | 7756 | 42 | 40 | 95.2381 | |
| rpoplin-dv42 | SNP | * | map_l250_m0_e0 | * | 97.4806 | 96.9555 | 98.0114 | 92.0139 | 2070 | 65 | 2070 | 42 | 27 | 64.2857 | |
| ltrigg-rtg2 | INDEL | D6_15 | HG002complexvar | hetalt | 94.0012 | 92.3001 | 95.7661 | 55.0113 | 935 | 78 | 950 | 42 | 42 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1175 | 98.9995 | 99.2358 | 63.1487 | 5541 | 56 | 5454 | 42 | 17 | 40.4762 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.9176 | 98.2314 | 99.6135 | 43.6336 | 10886 | 196 | 10826 | 42 | 39 | 92.8571 | |
| ltrigg-rtg2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.8441 | 99.5400 | 98.1579 | 64.3471 | 2164 | 10 | 2238 | 42 | 2 | 4.7619 | |
| ltrigg-rtg2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 98.2195 | 99.3511 | 97.1134 | 65.4886 | 1378 | 9 | 1413 | 42 | 2 | 4.7619 | |
| mlin-fermikit | INDEL | * | map_l125_m2_e1 | het | 67.5834 | 52.5568 | 94.6429 | 82.8559 | 740 | 668 | 742 | 42 | 17 | 40.4762 | |
| ndellapenna-hhga | INDEL | * | map_l100_m0_e0 | * | 97.2514 | 97.1849 | 97.3180 | 98.3412 | 1519 | 44 | 1524 | 42 | 9 | 21.4286 | |
| ndellapenna-hhga | INDEL | * | map_l125_m1_e0 | * | 97.7659 | 97.5320 | 98.0010 | 98.2503 | 2055 | 52 | 2059 | 42 | 15 | 35.7143 | |
| ndellapenna-hhga | INDEL | * | map_l125_m2_e0 | * | 97.8100 | 97.5410 | 98.0804 | 98.3346 | 2142 | 54 | 2146 | 42 | 15 | 35.7143 | |
| ndellapenna-hhga | INDEL | D1_5 | HG002complexvar | hetalt | 79.8795 | 68.7130 | 95.3795 | 77.9155 | 929 | 423 | 867 | 42 | 39 | 92.8571 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 74.0374 | 59.1106 | 99.0498 | 29.9414 | 4785 | 3310 | 4378 | 42 | 35 | 83.3333 | |
| ndellapenna-hhga | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 94.7368 | 93.2088 | 96.3158 | 71.7892 | 1098 | 80 | 1098 | 42 | 35 | 83.3333 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 90.2022 | 93.2476 | 87.3494 | 68.7382 | 290 | 21 | 290 | 42 | 36 | 85.7143 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 95.7480 | 95.8991 | 95.5975 | 81.7695 | 912 | 39 | 912 | 42 | 37 | 88.0952 | |
| ndellapenna-hhga | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.2992 | 97.3060 | 99.3129 | 66.5408 | 6068 | 168 | 6071 | 42 | 21 | 50.0000 | |
| ndellapenna-hhga | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.2051 | 98.7842 | 99.6296 | 37.6999 | 11294 | 139 | 11296 | 42 | 20 | 47.6190 | |
| ndellapenna-hhga | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.2708 | 98.9378 | 99.6061 | 37.1789 | 10618 | 114 | 10620 | 42 | 29 | 69.0476 | |