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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
25951-26000 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.3632 | 99.1908 | 99.5362 | 36.2528 | 1716 | 14 | 1717 | 8 | 6 | 75.0000 | |
| jlack-gatk | INDEL | D6_15 | map_l125_m0_e0 | * | 90.0000 | 95.7447 | 84.9057 | 94.0382 | 45 | 2 | 45 | 8 | 0 | 0.0000 | |
| jlack-gatk | INDEL | D6_15 | map_l150_m1_e0 | * | 93.4211 | 97.2603 | 89.8734 | 93.5668 | 71 | 2 | 71 | 8 | 0 | 0.0000 | |
| jlack-gatk | INDEL | D6_15 | map_l150_m2_e0 | * | 94.1176 | 97.5610 | 90.9091 | 93.6462 | 80 | 2 | 80 | 8 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I16_PLUS | * | hetalt | 92.9357 | 87.1306 | 99.5697 | 57.5280 | 1828 | 270 | 1851 | 8 | 7 | 87.5000 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 94.9161 | 93.4959 | 96.3801 | 87.9826 | 230 | 16 | 213 | 8 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 96.7604 | 97.5124 | 96.0199 | 87.0988 | 196 | 5 | 193 | 8 | 1 | 12.5000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.0242 | 95.4545 | 98.6464 | 64.6742 | 588 | 28 | 583 | 8 | 8 | 100.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | map_l100_m2_e0 | het | 89.8757 | 95.8333 | 84.6154 | 94.4622 | 46 | 2 | 44 | 8 | 2 | 25.0000 | |
| hfeng-pmm1 | INDEL | D16_PLUS | map_l100_m2_e1 | het | 90.4556 | 96.0784 | 85.4545 | 94.3123 | 49 | 2 | 47 | 8 | 2 | 25.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 94.2604 | 90.1484 | 98.7654 | 72.0930 | 668 | 73 | 640 | 8 | 6 | 75.0000 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l100_m0_e0 | * | 97.9502 | 96.8714 | 99.0533 | 81.2139 | 836 | 27 | 837 | 8 | 1 | 12.5000 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l125_m1_e0 | * | 98.0946 | 96.9669 | 99.2488 | 83.4909 | 1055 | 33 | 1057 | 8 | 1 | 12.5000 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l125_m2_e0 | * | 98.1873 | 97.1129 | 99.2857 | 84.4854 | 1110 | 33 | 1112 | 8 | 1 | 12.5000 | |
| hfeng-pmm1 | INDEL | D1_5 | map_l125_m2_e1 | * | 98.2094 | 97.1478 | 99.2945 | 84.5735 | 1124 | 33 | 1126 | 8 | 1 | 12.5000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.1595 | 95.6456 | 98.7220 | 86.6553 | 637 | 29 | 618 | 8 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.1595 | 95.6456 | 98.7220 | 86.6553 | 637 | 29 | 618 | 8 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.7564 | 96.8254 | 98.7055 | 66.0440 | 610 | 20 | 610 | 8 | 2 | 25.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | segdup | * | 99.1501 | 99.0557 | 99.2446 | 94.2109 | 1049 | 10 | 1051 | 8 | 2 | 25.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 91.9355 | 96.6102 | 87.6923 | 75.7463 | 57 | 2 | 57 | 8 | 8 | 100.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 97.5435 | 96.5174 | 98.5915 | 71.2841 | 582 | 21 | 560 | 8 | 4 | 50.0000 | |
| hfeng-pmm1 | SNP | * | HG002compoundhet | het | 96.0618 | 92.4743 | 99.9390 | 43.1383 | 13111 | 1067 | 13110 | 8 | 4 | 50.0000 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.8880 | 99.8233 | 99.9528 | 71.8323 | 16945 | 30 | 16945 | 8 | 5 | 62.5000 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.8880 | 99.8233 | 99.9528 | 71.8323 | 16945 | 30 | 16945 | 8 | 5 | 62.5000 | |
| hfeng-pmm1 | SNP | tv | map_l250_m1_e0 | homalt | 99.4179 | 99.7664 | 99.0719 | 87.2031 | 854 | 2 | 854 | 8 | 4 | 50.0000 | |
| hfeng-pmm1 | SNP | tv | map_l250_m2_e0 | homalt | 99.4146 | 99.6798 | 99.1507 | 88.0623 | 934 | 3 | 934 | 8 | 4 | 50.0000 | |
| hfeng-pmm1 | SNP | tv | map_l250_m2_e1 | homalt | 99.4201 | 99.6829 | 99.1588 | 88.1481 | 943 | 3 | 943 | 8 | 4 | 50.0000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.9418 | 94.1095 | 99.9498 | 41.0630 | 15721 | 984 | 15938 | 8 | 7 | 87.5000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.9418 | 94.1095 | 99.9498 | 41.0630 | 15721 | 984 | 15938 | 8 | 7 | 87.5000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.3740 | 98.3740 | 98.3740 | 59.0341 | 484 | 8 | 484 | 8 | 7 | 87.5000 | |
| hfeng-pmm2 | INDEL | * | map_l125_m2_e0 | homalt | 99.2157 | 99.4758 | 98.9570 | 85.4238 | 759 | 4 | 759 | 8 | 4 | 50.0000 | |
| hfeng-pmm2 | INDEL | * | map_l125_m2_e1 | homalt | 99.2268 | 99.4832 | 98.9717 | 85.5417 | 770 | 4 | 770 | 8 | 4 | 50.0000 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 89.8876 | 97.5610 | 83.3333 | 88.5167 | 40 | 1 | 40 | 8 | 7 | 87.5000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.1311 | 92.6743 | 99.8558 | 64.0650 | 5503 | 435 | 5540 | 8 | 7 | 87.5000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 71.0987 | 57.2816 | 93.7008 | 58.7662 | 118 | 88 | 119 | 8 | 2 | 25.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.0943 | 98.9524 | 99.2366 | 62.3968 | 1039 | 11 | 1040 | 8 | 7 | 87.5000 | |
| jlack-gatk | INDEL | I1_5 | map_siren | homalt | 99.3823 | 99.4224 | 99.3421 | 78.6217 | 1205 | 7 | 1208 | 8 | 5 | 62.5000 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.7191 | 97.1983 | 98.2456 | 71.4465 | 451 | 13 | 448 | 8 | 7 | 87.5000 | |
| jlack-gatk | INDEL | I6_15 | map_l100_m1_e0 | het | 89.2562 | 91.5254 | 87.0968 | 90.7186 | 54 | 5 | 54 | 8 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l100_m2_e0 | het | 89.6000 | 91.8033 | 87.5000 | 91.2688 | 56 | 5 | 56 | 8 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l100_m2_e1 | het | 89.6000 | 91.8033 | 87.5000 | 91.4894 | 56 | 5 | 56 | 8 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l125_m1_e0 | * | 88.0734 | 90.5660 | 85.7143 | 92.6606 | 48 | 5 | 48 | 8 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l125_m2_e0 | * | 88.0734 | 90.5660 | 85.7143 | 93.5409 | 48 | 5 | 48 | 8 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | map_l125_m2_e1 | * | 88.0734 | 90.5660 | 85.7143 | 93.7079 | 48 | 5 | 48 | 8 | 0 | 0.0000 | |
| jlack-gatk | INDEL | I6_15 | segdup | het | 94.1860 | 97.5904 | 91.0112 | 95.1419 | 81 | 2 | 81 | 8 | 0 | 0.0000 | |
| jlack-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.8960 | 99.8713 | 99.9208 | 48.6105 | 10089 | 13 | 10089 | 8 | 7 | 87.5000 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.2881 | 99.1766 | 99.3998 | 50.9385 | 1325 | 11 | 1325 | 8 | 0 | 0.0000 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.8869 | 98.7135 | 99.0610 | 53.7961 | 844 | 11 | 844 | 8 | 0 | 0.0000 | |
| jlack-gatk | SNP | tv | map_l100_m0_e0 | homalt | 99.0571 | 98.3359 | 99.7889 | 62.7592 | 3782 | 64 | 3782 | 8 | 5 | 62.5000 | |
| jlack-gatk | SNP | tv | map_l125_m0_e0 | homalt | 98.7279 | 97.8388 | 99.6332 | 70.1233 | 2173 | 48 | 2173 | 8 | 5 | 62.5000 | |