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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
30251-30300 / 86044 show all | |||||||||||||||
| asubramanian-gatk | INDEL | I1_5 | map_l100_m2_e0 | het | 87.2148 | 79.0668 | 97.2350 | 90.0428 | 627 | 166 | 633 | 18 | 2 | 11.1111 | |
| asubramanian-gatk | INDEL | I1_5 | map_l100_m2_e0 | homalt | 96.4050 | 93.4087 | 99.6000 | 83.0048 | 496 | 35 | 498 | 2 | 2 | 100.0000 | |
| asubramanian-gatk | INDEL | I1_5 | map_l100_m2_e1 | het | 87.1298 | 78.8889 | 97.2932 | 90.0657 | 639 | 171 | 647 | 18 | 2 | 11.1111 | |
| asubramanian-gatk | INDEL | I1_5 | map_l100_m2_e1 | homalt | 96.4668 | 93.5185 | 99.6071 | 83.0446 | 505 | 35 | 507 | 2 | 2 | 100.0000 | |
| asubramanian-gatk | INDEL | I1_5 | map_siren | homalt | 97.1653 | 94.7195 | 99.7407 | 79.1155 | 1148 | 64 | 1154 | 3 | 2 | 66.6667 | |
| asubramanian-gatk | INDEL | I1_5 | segdup | * | 98.7667 | 98.2059 | 99.3340 | 95.0336 | 1040 | 19 | 1044 | 7 | 2 | 28.5714 | |
| asubramanian-gatk | INDEL | I1_5 | segdup | homalt | 99.3644 | 99.1543 | 99.5754 | 92.7483 | 469 | 4 | 469 | 2 | 2 | 100.0000 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 98.1245 | 97.1074 | 99.1632 | 70.0501 | 235 | 7 | 237 | 2 | 2 | 100.0000 | |
| asubramanian-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 97.0588 | 97.0588 | 97.0588 | 71.0638 | 66 | 2 | 66 | 2 | 2 | 100.0000 | |
| asubramanian-gatk | INDEL | I6_15 | map_siren | homalt | 95.5056 | 94.4444 | 96.5909 | 86.3142 | 85 | 5 | 85 | 3 | 2 | 66.6667 | |
| asubramanian-gatk | SNP | * | * | hetalt | 94.8157 | 94.4891 | 95.1445 | 47.6709 | 823 | 48 | 823 | 42 | 2 | 4.7619 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.0423 | 98.7194 | 99.3672 | 50.0468 | 4240 | 55 | 4240 | 27 | 2 | 7.4074 | |
| asubramanian-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 97.8328 | 99.0038 | 96.6891 | 76.0765 | 3876 | 39 | 3884 | 133 | 2 | 1.5038 | |
| asubramanian-gatk | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.0021 | 98.8951 | 99.1093 | 37.8896 | 4565 | 51 | 4562 | 41 | 2 | 4.8781 | |
| asubramanian-gatk | SNP | * | map_siren | homalt | 73.1014 | 57.6093 | 99.9906 | 63.4885 | 31775 | 23381 | 31766 | 3 | 2 | 66.6667 | |
| asubramanian-gatk | SNP | * | tech_badpromoters | * | 98.4026 | 98.0892 | 98.7179 | 49.3506 | 154 | 3 | 154 | 2 | 2 | 100.0000 | |
| asubramanian-gatk | SNP | * | tech_badpromoters | homalt | 98.1366 | 98.7500 | 97.5309 | 46.7105 | 79 | 1 | 79 | 2 | 2 | 100.0000 | |
| asubramanian-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.4277 | 98.8814 | 99.9800 | 49.5688 | 9989 | 113 | 9998 | 2 | 2 | 100.0000 | |
| asubramanian-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.1337 | 98.6144 | 99.6585 | 48.5413 | 2918 | 41 | 2918 | 10 | 2 | 20.0000 | |
| asubramanian-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0572 | 98.8725 | 99.2426 | 41.5382 | 10611 | 121 | 10614 | 81 | 2 | 2.4691 | |
| asubramanian-gatk | SNP | ti | map_l150_m0_e0 | * | 32.0231 | 19.0688 | 99.8668 | 96.6434 | 1499 | 6362 | 1499 | 2 | 2 | 100.0000 | |
| asubramanian-gatk | SNP | ti | map_l150_m0_e0 | het | 34.9037 | 21.1497 | 99.8148 | 97.0413 | 1078 | 4019 | 1078 | 2 | 2 | 100.0000 | |
| anovak-vg | INDEL | I1_5 | tech_badpromoters | homalt | 72.8745 | 69.2308 | 76.9231 | 40.9091 | 9 | 4 | 10 | 3 | 2 | 66.6667 | |
| anovak-vg | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 4.0816 | 2.1739 | 33.3333 | 62.5000 | 2 | 90 | 2 | 4 | 2 | 50.0000 | |
| anovak-vg | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 16.6667 | 11.1111 | 33.3333 | 57.1429 | 1 | 8 | 2 | 4 | 2 | 50.0000 | |
| anovak-vg | INDEL | I6_15 | map_l125_m0_e0 | homalt | 78.9474 | 83.3333 | 75.0000 | 87.8788 | 5 | 1 | 6 | 2 | 2 | 100.0000 | |
| anovak-vg | INDEL | I6_15 | map_l125_m1_e0 | het | 53.8462 | 46.6667 | 63.6364 | 86.1925 | 14 | 16 | 21 | 12 | 2 | 16.6667 | |
| anovak-vg | INDEL | I6_15 | map_l125_m2_e0 | het | 53.8462 | 46.6667 | 63.6364 | 87.4046 | 14 | 16 | 21 | 12 | 2 | 16.6667 | |
| anovak-vg | INDEL | I6_15 | map_l125_m2_e1 | het | 53.8462 | 46.6667 | 63.6364 | 87.6866 | 14 | 16 | 21 | 12 | 2 | 16.6667 | |
| anovak-vg | INDEL | I6_15 | map_l150_m1_e0 | * | 61.4458 | 60.0000 | 62.9630 | 91.0299 | 15 | 10 | 17 | 10 | 2 | 20.0000 | |
| anovak-vg | INDEL | I6_15 | map_l150_m2_e0 | * | 61.4458 | 60.0000 | 62.9630 | 92.1283 | 15 | 10 | 17 | 10 | 2 | 20.0000 | |
| anovak-vg | INDEL | I6_15 | map_l150_m2_e1 | homalt | 73.8462 | 75.0000 | 72.7273 | 91.6667 | 6 | 2 | 8 | 3 | 2 | 66.6667 | |
| anovak-vg | INDEL | I6_15 | tech_badpromoters | * | 57.1429 | 46.1538 | 75.0000 | 50.0000 | 6 | 7 | 6 | 2 | 2 | 100.0000 | |
| anovak-vg | INDEL | I6_15 | tech_badpromoters | homalt | 75.0000 | 100.0000 | 60.0000 | 54.5455 | 3 | 0 | 3 | 2 | 2 | 100.0000 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_triTR_51to200 | het | 65.2174 | 71.4286 | 60.0000 | 94.8454 | 5 | 2 | 6 | 4 | 2 | 50.0000 | |
| anovak-vg | SNP | ti | lowcmp_SimpleRepeat_diTR_51to200 | het | 73.2984 | 70.0000 | 76.9231 | 96.4674 | 7 | 3 | 10 | 3 | 2 | 66.6667 | |
| anovak-vg | SNP | ti | lowcmp_SimpleRepeat_triTR_51to200 | * | 62.5000 | 62.5000 | 62.5000 | 94.8718 | 5 | 3 | 5 | 3 | 2 | 66.6667 | |
| anovak-vg | SNP | ti | tech_badpromoters | het | 83.5443 | 75.0000 | 94.2857 | 45.3125 | 33 | 11 | 33 | 2 | 2 | 100.0000 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | het | 90.5425 | 92.0000 | 89.1304 | 86.3905 | 46 | 4 | 41 | 5 | 2 | 40.0000 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | homalt | 97.9167 | 100.0000 | 95.9184 | 54.2056 | 47 | 0 | 47 | 2 | 2 | 100.0000 | |
| astatham-gatk | INDEL | * | map_l125_m0_e0 | het | 95.6440 | 95.2300 | 96.0616 | 91.1381 | 559 | 28 | 561 | 23 | 2 | 8.6957 | |
| astatham-gatk | INDEL | * | map_l250_m0_e0 | * | 90.3614 | 96.1538 | 85.2273 | 97.7873 | 75 | 3 | 75 | 13 | 2 | 15.3846 | |
| astatham-gatk | INDEL | * | map_l250_m1_e0 | het | 93.5733 | 95.7895 | 91.4573 | 96.4356 | 182 | 8 | 182 | 17 | 2 | 11.7647 | |
| astatham-gatk | INDEL | * | map_l250_m1_e0 | homalt | 97.7169 | 98.1651 | 97.2727 | 94.9192 | 107 | 2 | 107 | 3 | 2 | 66.6667 | |
| astatham-gatk | INDEL | * | map_l250_m2_e0 | het | 93.9252 | 95.7143 | 92.2018 | 96.5943 | 201 | 9 | 201 | 17 | 2 | 11.7647 | |
| astatham-gatk | INDEL | * | map_l250_m2_e0 | homalt | 97.8355 | 98.2609 | 97.4138 | 95.3432 | 113 | 2 | 113 | 3 | 2 | 66.6667 | |
| astatham-gatk | INDEL | * | map_l250_m2_e1 | het | 93.9535 | 95.7346 | 92.2374 | 96.6702 | 202 | 9 | 202 | 17 | 2 | 11.7647 | |
| astatham-gatk | INDEL | * | map_l250_m2_e1 | homalt | 97.8541 | 98.2759 | 97.4359 | 95.4333 | 114 | 2 | 114 | 3 | 2 | 66.6667 | |
| astatham-gatk | INDEL | * | segdup | het | 98.4019 | 98.7040 | 98.1017 | 95.1947 | 1447 | 19 | 1447 | 28 | 2 | 7.1429 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 98.0494 | 98.1771 | 97.9221 | 86.1908 | 377 | 7 | 377 | 8 | 2 | 25.0000 | |