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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
14701-14750 / 86044 show all | |||||||||||||||
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 95.4738 | 95.6357 | 95.3125 | 79.8742 | 504 | 23 | 427 | 21 | 20 | 95.2381 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.4745 | 99.8312 | 99.1202 | 49.1587 | 2366 | 4 | 2366 | 21 | 20 | 95.2381 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 96.2500 | 99.0354 | 93.6170 | 69.7610 | 308 | 3 | 308 | 21 | 20 | 95.2381 | |
| jlack-gatk | SNP | ti | map_l250_m0_e0 | * | 92.5591 | 97.1533 | 88.3798 | 95.5349 | 1331 | 39 | 1331 | 175 | 20 | 11.4286 | |
| jlack-gatk | SNP | ti | map_siren | homalt | 99.6031 | 99.2879 | 99.9204 | 49.0602 | 37646 | 270 | 37640 | 30 | 20 | 66.6667 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.2477 | 99.2381 | 99.2572 | 75.1119 | 5080 | 39 | 5078 | 38 | 20 | 52.6316 | |
| jlack-gatk | INDEL | * | map_l100_m1_e0 | het | 93.6574 | 98.2103 | 89.5079 | 89.1540 | 2195 | 40 | 2201 | 258 | 20 | 7.7519 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 96.0876 | 98.7138 | 93.5976 | 68.7321 | 307 | 4 | 307 | 21 | 20 | 95.2381 | |
| hfeng-pmm1 | SNP | ti | map_l100_m1_e0 | het | 99.3951 | 99.0615 | 99.7309 | 63.4093 | 29661 | 281 | 29654 | 80 | 20 | 25.0000 | |
| hfeng-pmm1 | SNP | ti | map_l100_m2_e0 | het | 99.3987 | 99.0660 | 99.7336 | 64.8032 | 30336 | 286 | 30329 | 81 | 20 | 24.6914 | |
| hfeng-pmm1 | SNP | ti | map_l100_m2_e1 | het | 99.4037 | 99.0762 | 99.7333 | 64.8020 | 30674 | 286 | 30667 | 82 | 20 | 24.3902 | |
| hfeng-pmm1 | SNP | ti | map_l125_m0_e0 | * | 99.2424 | 99.0519 | 99.4336 | 73.9101 | 12641 | 121 | 12639 | 72 | 20 | 27.7778 | |
| hfeng-pmm1 | SNP | tv | HG002complexvar | * | 99.8458 | 99.7087 | 99.9833 | 21.6860 | 245435 | 717 | 245349 | 41 | 20 | 48.7805 | |
| hfeng-pmm1 | SNP | * | HG002complexvar | het | 99.8138 | 99.6436 | 99.9845 | 18.0286 | 463838 | 1659 | 463708 | 72 | 19 | 26.3889 | |
| hfeng-pmm1 | SNP | tv | * | het | 99.9077 | 99.8553 | 99.9601 | 20.8554 | 590840 | 856 | 590766 | 236 | 19 | 8.0509 | |
| hfeng-pmm2 | SNP | * | map_l100_m1_e0 | homalt | 99.8648 | 99.8704 | 99.8593 | 60.9853 | 26968 | 35 | 26968 | 38 | 19 | 50.0000 | |
| hfeng-pmm2 | SNP | * | map_l100_m2_e0 | homalt | 99.8674 | 99.8728 | 99.8619 | 63.3992 | 27488 | 35 | 27488 | 38 | 19 | 50.0000 | |
| hfeng-pmm2 | SNP | * | map_l100_m2_e1 | homalt | 99.8687 | 99.8741 | 99.8633 | 63.3911 | 27761 | 35 | 27761 | 38 | 19 | 50.0000 | |
| hfeng-pmm2 | SNP | * | map_l150_m0_e0 | * | 98.8358 | 99.1523 | 98.5214 | 81.5215 | 11930 | 102 | 11927 | 179 | 19 | 10.6145 | |
| hfeng-pmm2 | SNP | ti | map_l100_m0_e0 | * | 99.3277 | 99.4212 | 99.2343 | 69.9178 | 21645 | 126 | 21642 | 167 | 19 | 11.3772 | |
| hfeng-pmm2 | SNP | ti | map_siren | het | 99.5502 | 99.5223 | 99.5781 | 56.1068 | 62084 | 298 | 62075 | 263 | 19 | 7.2243 | |
| hfeng-pmm3 | INDEL | D1_5 | HG002complexvar | * | 99.2121 | 98.5267 | 99.9072 | 56.6840 | 32233 | 482 | 32285 | 30 | 19 | 63.3333 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.4735 | 88.5110 | 99.0255 | 55.9755 | 2134 | 277 | 2134 | 21 | 19 | 90.4762 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5480 | 99.6325 | 99.4637 | 71.3697 | 3524 | 13 | 3524 | 19 | 19 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.6812 | 95.9164 | 99.5121 | 62.7887 | 5097 | 217 | 5099 | 25 | 19 | 76.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 80.5324 | 69.4405 | 95.8416 | 48.3640 | 484 | 213 | 484 | 21 | 19 | 90.4762 | |
| jlack-gatk | INDEL | D6_15 | HG002complexvar | homalt | 99.0234 | 99.7434 | 98.3137 | 61.3807 | 1166 | 3 | 1166 | 20 | 19 | 95.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.5017 | 97.5265 | 93.5593 | 68.9474 | 276 | 7 | 276 | 19 | 19 | 100.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 86.1314 | 100.0000 | 75.6410 | 73.7374 | 59 | 0 | 59 | 19 | 19 | 100.0000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.6568 | 96.9051 | 98.4202 | 76.2358 | 1910 | 61 | 1869 | 30 | 19 | 63.3333 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.6568 | 96.9051 | 98.4202 | 76.2358 | 1910 | 61 | 1869 | 30 | 19 | 63.3333 | |
| jlack-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.4079 | 99.8008 | 97.0534 | 66.9969 | 17533 | 35 | 17523 | 532 | 19 | 3.5714 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7466 | 99.5860 | 99.9077 | 57.3042 | 28143 | 117 | 28146 | 26 | 19 | 73.0769 | |
| gduggal-bwavard | INDEL | I1_5 | map_l125_m1_e0 | het | 94.3995 | 98.1481 | 90.9266 | 90.6464 | 477 | 9 | 471 | 47 | 19 | 40.4255 | |
| gduggal-bwavard | INDEL | I6_15 | map_l100_m1_e0 | * | 71.7489 | 70.1754 | 73.3945 | 86.6585 | 80 | 34 | 80 | 29 | 19 | 65.5172 | |
| gduggal-bwavard | INDEL | I6_15 | map_l100_m1_e0 | het | 78.3217 | 94.9153 | 66.6667 | 88.3978 | 56 | 3 | 56 | 28 | 19 | 67.8571 | |
| gduggal-bwavard | INDEL | I6_15 | map_l100_m2_e0 | * | 72.2467 | 70.6897 | 73.8739 | 87.7212 | 82 | 34 | 82 | 29 | 19 | 65.5172 | |
| gduggal-bwavard | INDEL | I6_15 | map_l100_m2_e0 | het | 78.9116 | 95.0820 | 67.4419 | 89.1960 | 58 | 3 | 58 | 28 | 19 | 67.8571 | |
| gduggal-bwavard | INDEL | I6_15 | map_l100_m2_e1 | * | 72.2467 | 70.6897 | 73.8739 | 87.9870 | 82 | 34 | 82 | 29 | 19 | 65.5172 | |
| gduggal-bwavard | INDEL | I6_15 | map_l100_m2_e1 | het | 78.9116 | 95.0820 | 67.4419 | 89.4349 | 58 | 3 | 58 | 28 | 19 | 67.8571 | |
| gduggal-bwavard | SNP | * | HG002compoundhet | homalt | 91.3621 | 84.3072 | 99.7055 | 35.4356 | 9090 | 1692 | 7788 | 23 | 19 | 82.6087 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.2853 | 97.2759 | 95.3147 | 68.9687 | 4178 | 117 | 4150 | 204 | 19 | 9.3137 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 94.9992 | 97.3939 | 92.7195 | 74.6356 | 2616 | 70 | 2598 | 204 | 19 | 9.3137 | |
| gduggal-bwavard | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 98.0250 | 97.6820 | 98.3704 | 46.6267 | 4509 | 107 | 4467 | 74 | 19 | 25.6757 | |
| gduggal-bwavard | SNP | tv | segdup | homalt | 98.3926 | 97.4676 | 99.3354 | 90.2442 | 3156 | 82 | 3139 | 21 | 19 | 90.4762 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 88.8144 | 80.8349 | 98.5418 | 47.2042 | 426 | 101 | 1284 | 19 | 19 | 100.0000 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 80.7025 | 72.6989 | 90.6863 | 50.9615 | 466 | 175 | 185 | 19 | 19 | 100.0000 | |
| gduggal-bwafb | SNP | * | map_l100_m1_e0 | homalt | 99.5971 | 99.3186 | 99.8771 | 62.3452 | 26819 | 184 | 26819 | 33 | 19 | 57.5758 | |
| gduggal-bwavard | INDEL | C6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 73.9336 | 100.0000 | 58.6466 | 95.6607 | 1 | 0 | 78 | 55 | 19 | 34.5455 | |
| gduggal-bwavard | INDEL | D1_5 | map_l125_m1_e0 | * | 92.4713 | 96.7831 | 88.5274 | 88.5445 | 1053 | 35 | 1034 | 134 | 19 | 14.1791 | |