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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
25651-25700 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.2920 | 98.4666 | 96.1450 | 64.1784 | 12329 | 192 | 12171 | 488 | 413 | 84.6311 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 95.6093 | 91.9316 | 99.5935 | 30.0616 | 10209 | 896 | 10290 | 42 | 37 | 88.0952 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 97.7765 | 99.6055 | 96.0134 | 48.3178 | 8333 | 33 | 8333 | 346 | 344 | 99.4220 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 96.1122 | 95.6040 | 96.6259 | 60.2914 | 41430 | 1905 | 41238 | 1440 | 1303 | 90.4861 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 96.7207 | 98.0134 | 95.4617 | 70.0763 | 17465 | 354 | 17080 | 812 | 691 | 85.0985 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 94.2610 | 89.4954 | 99.5627 | 34.0219 | 12558 | 1474 | 12751 | 56 | 50 | 89.2857 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 97.2339 | 99.3295 | 95.2250 | 57.6340 | 11407 | 77 | 11407 | 572 | 562 | 98.2517 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.8694 | 96.4285 | 97.3143 | 66.9705 | 63017 | 2334 | 62795 | 1733 | 1467 | 84.6509 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.3816 | 98.0381 | 96.7339 | 73.7893 | 29882 | 598 | 29440 | 994 | 753 | 75.7545 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 94.6842 | 90.2604 | 99.5639 | 40.3949 | 15078 | 1627 | 15298 | 67 | 60 | 89.5522 | |
| jlack-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.8832 | 99.4000 | 96.4120 | 64.9755 | 18057 | 109 | 18057 | 672 | 654 | 97.3214 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.2911 | 96.9146 | 97.6705 | 52.3019 | 35463 | 1129 | 35387 | 844 | 761 | 90.1659 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.7311 | 98.5279 | 96.9471 | 62.1515 | 15528 | 232 | 15370 | 484 | 412 | 85.1240 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 95.4742 | 91.7900 | 99.4666 | 33.0334 | 9615 | 860 | 9697 | 52 | 46 | 88.4615 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.3560 | 99.6428 | 97.1020 | 45.5337 | 10320 | 37 | 10320 | 308 | 303 | 98.3766 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 74.6828 | 72.3465 | 77.1751 | 57.2642 | 1520 | 581 | 1437 | 425 | 403 | 94.8235 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | het | 63.1909 | 86.1224 | 49.9033 | 76.4142 | 422 | 68 | 258 | 259 | 240 | 92.6641 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 75.7194 | 61.1022 | 99.5294 | 32.2169 | 765 | 487 | 846 | 4 | 3 | 75.0000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 77.9859 | 92.7577 | 67.2727 | 45.6641 | 333 | 26 | 333 | 162 | 160 | 98.7654 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_gt200 | * | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_gt200 | het | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_gt200 | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_gt200 | homalt | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7099 | 99.7098 | 99.7099 | 59.0011 | 28178 | 82 | 28181 | 82 | 31 | 37.8049 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.6624 | 99.7383 | 99.5867 | 60.0529 | 16386 | 43 | 16385 | 68 | 18 | 26.4706 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 97.2503 | 95.7009 | 98.8506 | 74.0943 | 512 | 23 | 516 | 6 | 6 | 100.0000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.8937 | 99.8584 | 99.9291 | 56.1359 | 11280 | 16 | 11280 | 8 | 7 | 87.5000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 52.6631 | 81.4516 | 38.9105 | 99.8116 | 101 | 23 | 100 | 157 | 5 | 3.1847 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 45.6361 | 81.6092 | 31.6742 | 99.7077 | 71 | 16 | 70 | 151 | 4 | 2.6490 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | hetalt | 76.4706 | 81.2500 | 72.2222 | 99.8592 | 13 | 3 | 13 | 5 | 0 | 0.0000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | homalt | 87.1795 | 80.9524 | 94.4444 | 99.9625 | 17 | 4 | 17 | 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 | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9876 | 99.1538 | 98.8219 | 62.9494 | 11014 | 94 | 10989 | 131 | 41 | 31.2977 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.0087 | 96.3087 | 99.7699 | 41.5864 | 2583 | 99 | 2601 | 6 | 6 | 100.0000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.4911 | 99.8188 | 99.1656 | 57.1479 | 6061 | 11 | 6061 | 51 | 49 | 96.0784 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.1564 | 95.4426 | 96.8811 | 68.1564 | 2534 | 121 | 2485 | 80 | 69 | 86.2500 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 96.0781 | 96.4876 | 95.6720 | 82.3695 | 934 | 34 | 840 | 38 | 30 | 78.9474 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 95.9073 | 92.8033 | 99.2261 | 33.2760 | 1109 | 86 | 1154 | 9 | 8 | 88.8889 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 96.6535 | 99.7967 | 93.7023 | 60.6607 | 491 | 1 | 491 | 33 | 31 | 93.9394 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_gt200 | * | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_gt200 | het | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_gt200 | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 0 | 0 | 0 | 0 | |||
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_gt200 | homalt | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.5542 | 99.4802 | 99.6283 | 49.3638 | 6698 | 35 | 6700 | 25 | 14 | 56.0000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.5350 | 99.4806 | 99.5894 | 54.0098 | 3639 | 19 | 3638 | 15 | 5 | 33.3333 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.2378 | 98.6999 | 99.7817 | 29.1570 | 911 | 12 | 914 | 2 | 2 | 100.0000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.7214 | 99.8141 | 99.6289 | 46.6996 | 2148 | 4 | 2148 | 8 | 7 | 87.5000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 94.4550 | 92.3423 | 96.6667 | 63.0282 | 205 | 17 | 203 | 7 | 7 | 100.0000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | het | 91.6509 | 92.0000 | 91.3043 | 85.0649 | 46 | 4 | 42 | 4 | 4 | 100.0000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 94.5148 | 89.6000 | 100.0000 | 27.8481 | 112 | 13 | 114 | 0 | 0 | ||