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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
76051-76100 / 86044 show all | |||||||||||||||
| gduggal-bwavard | INDEL | * | map_l150_m2_e1 | * | 90.5345 | 95.2745 | 86.2437 | 91.9653 | 1371 | 68 | 1373 | 219 | 51 | 23.2877 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m2_e1 | * | 92.7581 | 94.9974 | 90.6219 | 86.9648 | 1842 | 97 | 1807 | 187 | 51 | 27.2727 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 55.9006 | 50.5618 | 62.5000 | 73.6264 | 90 | 88 | 90 | 54 | 51 | 94.4444 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 70.1923 | 90.1235 | 57.4803 | 74.8016 | 73 | 8 | 73 | 54 | 51 | 94.4444 | |
| gduggal-bwavard | SNP | tv | map_l150_m2_e1 | * | 94.1240 | 97.9830 | 90.5575 | 83.2923 | 11270 | 232 | 11240 | 1172 | 51 | 4.3515 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.7954 | 98.2348 | 99.3624 | 57.2660 | 16139 | 290 | 16208 | 104 | 51 | 49.0385 | |
| eyeh-varpipe | SNP | * | map_l100_m1_e0 | * | 98.6894 | 99.7348 | 97.6657 | 67.8112 | 72211 | 192 | 69996 | 1673 | 51 | 3.0484 | |
| eyeh-varpipe | SNP | * | map_l100_m2_e0 | * | 98.6905 | 99.7377 | 97.6651 | 69.5065 | 73770 | 194 | 71526 | 1710 | 51 | 2.9825 | |
| eyeh-varpipe | SNP | * | map_l100_m2_e1 | * | 98.6948 | 99.7404 | 97.6710 | 69.5344 | 74543 | 194 | 72256 | 1723 | 51 | 2.9600 | |
| eyeh-varpipe | SNP | * | map_siren | het | 98.0835 | 99.7637 | 96.4589 | 61.2396 | 90776 | 215 | 87713 | 3220 | 51 | 1.5839 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.8642 | 99.2036 | 98.5271 | 69.1157 | 11460 | 92 | 11104 | 166 | 51 | 30.7229 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.8642 | 99.2036 | 98.5271 | 69.1157 | 11460 | 92 | 11104 | 166 | 51 | 30.7229 | |
| gduggal-bwaplat | INDEL | I16_PLUS | * | homalt | 87.5361 | 80.5253 | 95.8841 | 57.8947 | 1257 | 304 | 1258 | 54 | 51 | 94.4444 | |
| gduggal-bwafb | SNP | tv | map_l125_m2_e0 | * | 98.6658 | 98.8902 | 98.4424 | 74.7627 | 16306 | 183 | 16306 | 258 | 51 | 19.7674 | |
| gduggal-bwafb | SNP | tv | map_l125_m2_e1 | * | 98.6792 | 98.9014 | 98.4580 | 74.8361 | 16474 | 183 | 16474 | 258 | 51 | 19.7674 | |
| gduggal-bwaplat | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 78.4779 | 66.1838 | 96.3816 | 73.7433 | 1462 | 747 | 1465 | 55 | 51 | 92.7273 | |
| eyeh-varpipe | INDEL | C6_15 | * | * | 89.4022 | 100.0000 | 80.8354 | 93.6057 | 7 | 0 | 329 | 78 | 51 | 65.3846 | |
| ltrigg-rtg1 | INDEL | D1_5 | HG002complexvar | hetalt | 94.6417 | 92.8994 | 96.4505 | 77.3885 | 1256 | 96 | 1413 | 52 | 51 | 98.0769 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.3079 | 97.1210 | 99.5241 | 52.9586 | 15585 | 462 | 15476 | 74 | 51 | 68.9189 | |
| jpowers-varprowl | INDEL | * | map_l150_m1_e0 | * | 92.4886 | 91.1061 | 93.9137 | 90.2023 | 1219 | 119 | 1219 | 79 | 51 | 64.5570 | |
| jpowers-varprowl | INDEL | * | map_l150_m2_e1 | het | 92.1590 | 92.8571 | 91.4712 | 91.9353 | 858 | 66 | 858 | 80 | 51 | 63.7500 | |
| jpowers-varprowl | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 96.4333 | 99.6568 | 93.4119 | 74.1305 | 1742 | 6 | 1744 | 123 | 51 | 41.4634 | |
| jli-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 95.6451 | 94.1259 | 97.2141 | 69.2007 | 2003 | 125 | 1989 | 57 | 51 | 89.4737 | |
| jli-custom | INDEL | I16_PLUS | * | * | 96.2725 | 93.9627 | 98.6987 | 64.2188 | 5992 | 385 | 5992 | 79 | 51 | 64.5570 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.4779 | 95.9039 | 99.1043 | 49.4530 | 6626 | 283 | 6639 | 60 | 51 | 85.0000 | |
| jmaeng-gatk | SNP | * | map_l125_m1_e0 | het | 88.1536 | 81.0158 | 96.6706 | 86.7253 | 23002 | 5390 | 22996 | 792 | 51 | 6.4394 | |
| jmaeng-gatk | SNP | * | map_l125_m2_e0 | het | 88.4835 | 81.5574 | 96.6953 | 87.4762 | 23911 | 5407 | 23905 | 817 | 51 | 6.2424 | |
| ltrigg-rtg1 | SNP | * | segdup | * | 99.0787 | 99.6188 | 98.5445 | 88.0967 | 27960 | 107 | 27963 | 413 | 51 | 12.3487 | |
| ltrigg-rtg2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.3655 | 97.3387 | 99.4143 | 58.7428 | 14228 | 389 | 14257 | 84 | 51 | 60.7143 | |
| hfeng-pmm3 | INDEL | I1_5 | * | het | 99.7016 | 99.5433 | 99.8604 | 59.2337 | 78680 | 361 | 78661 | 110 | 51 | 46.3636 | |
| hfeng-pmm1 | INDEL | D1_5 | * | het | 99.5580 | 99.2715 | 99.8461 | 55.4481 | 86936 | 638 | 86940 | 134 | 51 | 38.0597 | |
| hfeng-pmm1 | SNP | * | HG002complexvar | * | 99.8780 | 99.7704 | 99.9859 | 18.8078 | 752649 | 1732 | 752504 | 106 | 51 | 48.1132 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 94.6034 | 94.8872 | 94.3212 | 81.3996 | 1262 | 68 | 1063 | 64 | 51 | 79.6875 | |
| hfeng-pmm2 | INDEL | I16_PLUS | * | homalt | 98.0751 | 99.5516 | 96.6418 | 69.9214 | 1554 | 7 | 1554 | 54 | 51 | 94.4444 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 92.1621 | 97.7230 | 87.2000 | 81.7983 | 515 | 12 | 436 | 64 | 51 | 79.6875 | |
| qzeng-custom | INDEL | I16_PLUS | HG002complexvar | * | 86.4583 | 83.8044 | 89.2857 | 60.9632 | 1097 | 212 | 1100 | 132 | 51 | 38.6364 | |
| ndellapenna-hhga | SNP | * | segdup | * | 99.5371 | 99.5903 | 99.4839 | 89.2221 | 27952 | 115 | 27952 | 145 | 51 | 35.1724 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5119 | 97.7585 | 99.2769 | 36.5690 | 9246 | 212 | 9199 | 67 | 51 | 76.1194 | |
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 98.6157 | 98.5123 | 98.7194 | 55.0135 | 6092 | 92 | 6090 | 79 | 51 | 64.5570 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 55.7555 | 54.6245 | 56.9343 | 95.0071 | 691 | 574 | 702 | 531 | 51 | 9.6045 | |
| gduggal-snapplat | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 42.3946 | 28.6024 | 81.8750 | 58.3875 | 264 | 659 | 262 | 58 | 51 | 87.9310 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 28.9593 | 17.5631 | 82.4742 | 66.3778 | 320 | 1502 | 320 | 68 | 51 | 75.0000 | |
| gduggal-snapvard | INDEL | I1_5 | HG002complexvar | homalt | 92.5606 | 86.5333 | 99.4905 | 33.4524 | 11637 | 1811 | 10935 | 56 | 51 | 91.0714 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 88.5630 | 82.2103 | 95.9796 | 32.1478 | 5661 | 1225 | 1886 | 79 | 51 | 64.5570 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 57.4519 | 55.8442 | 59.1549 | 62.6561 | 215 | 170 | 336 | 232 | 51 | 21.9828 | |
| ghariani-varprowl | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 76.1858 | 63.3364 | 95.5758 | 45.0405 | 1363 | 789 | 1361 | 63 | 51 | 80.9524 | |
| ghariani-varprowl | INDEL | * | map_l150_m1_e0 | * | 90.8174 | 94.2451 | 87.6303 | 95.0045 | 1261 | 77 | 1261 | 178 | 51 | 28.6517 | |
| ghariani-varprowl | SNP | ti | map_l250_m2_e1 | het | 95.1903 | 97.7872 | 92.7278 | 92.3245 | 3226 | 73 | 3226 | 253 | 51 | 20.1581 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 92.5148 | 92.3810 | 92.6491 | 58.3237 | 679 | 56 | 668 | 53 | 51 | 96.2264 | |
| anovak-vg | INDEL | I1_5 | map_l150_m0_e0 | * | 58.6797 | 59.6591 | 57.7320 | 93.8118 | 105 | 71 | 112 | 82 | 51 | 62.1951 | |