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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
30751-30800 / 86044 show all | |||||||||||||||
| hfeng-pmm3 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 80.0000 | 100.0000 | 66.6667 | 88.8889 | 4 | 0 | 4 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | * | hetalt | 97.1290 | 94.4350 | 99.9812 | 61.2138 | 10572 | 623 | 10632 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | HG002complexvar | hetalt | 98.0250 | 96.2341 | 99.8839 | 70.2777 | 1661 | 65 | 1721 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.8615 | 98.0480 | 99.6885 | 70.4692 | 1306 | 26 | 1280 | 4 | 2 | 50.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6041 | 99.3604 | 99.8489 | 69.0699 | 2641 | 17 | 2643 | 4 | 2 | 50.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.8968 | 100.0000 | 99.7938 | 63.5064 | 968 | 0 | 968 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.4393 | 99.6255 | 99.2537 | 63.5870 | 266 | 1 | 266 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l125_m0_e0 | * | 98.5533 | 98.7097 | 98.3974 | 87.4598 | 306 | 4 | 307 | 5 | 2 | 40.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l125_m0_e0 | homalt | 98.7013 | 100.0000 | 97.4359 | 83.1412 | 114 | 0 | 114 | 3 | 2 | 66.6667 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l125_m1_e0 | * | 98.9155 | 98.7952 | 99.0361 | 84.0996 | 820 | 10 | 822 | 8 | 2 | 25.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l125_m1_e0 | homalt | 99.5434 | 100.0000 | 99.0909 | 81.2073 | 327 | 0 | 327 | 3 | 2 | 66.6667 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l125_m2_e0 | * | 98.8315 | 98.5998 | 99.0643 | 85.4245 | 845 | 12 | 847 | 8 | 2 | 25.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l125_m2_e0 | homalt | 99.5620 | 100.0000 | 99.1279 | 82.7569 | 341 | 0 | 341 | 3 | 2 | 66.6667 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l125_m2_e1 | * | 98.8490 | 98.6207 | 99.0783 | 85.5790 | 858 | 12 | 860 | 8 | 2 | 25.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l125_m2_e1 | homalt | 99.5646 | 100.0000 | 99.1329 | 83.0475 | 343 | 0 | 343 | 3 | 2 | 66.6667 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l150_m0_e0 | * | 98.0105 | 97.7273 | 98.2955 | 90.9558 | 172 | 4 | 173 | 3 | 2 | 66.6667 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l150_m0_e0 | homalt | 98.5294 | 100.0000 | 97.1014 | 86.8821 | 67 | 0 | 67 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l150_m1_e0 | * | 98.4221 | 98.4190 | 98.4252 | 87.6729 | 498 | 8 | 500 | 8 | 2 | 25.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l150_m1_e0 | homalt | 99.2481 | 100.0000 | 98.5075 | 84.9099 | 198 | 0 | 198 | 3 | 2 | 66.6667 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l150_m2_e0 | * | 98.3636 | 98.2659 | 98.4615 | 88.9078 | 510 | 9 | 512 | 8 | 2 | 25.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l150_m2_e0 | homalt | 99.2593 | 100.0000 | 98.5294 | 86.7961 | 201 | 0 | 201 | 3 | 2 | 66.6667 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l150_m2_e1 | * | 98.4006 | 98.3051 | 98.4962 | 88.9741 | 522 | 9 | 524 | 8 | 2 | 25.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l150_m2_e1 | homalt | 99.2701 | 100.0000 | 98.5507 | 86.9318 | 204 | 0 | 204 | 3 | 2 | 66.6667 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l250_m1_e0 | * | 96.7136 | 97.1698 | 96.2617 | 95.2168 | 103 | 3 | 103 | 4 | 2 | 50.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l250_m1_e0 | homalt | 97.7778 | 100.0000 | 95.6522 | 92.9339 | 44 | 0 | 44 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l250_m2_e0 | * | 96.9163 | 97.3451 | 96.4912 | 95.6472 | 110 | 3 | 110 | 4 | 2 | 50.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l250_m2_e0 | homalt | 97.8261 | 100.0000 | 95.7447 | 93.9666 | 45 | 0 | 45 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l250_m2_e1 | * | 96.9432 | 97.3684 | 96.5217 | 95.7407 | 111 | 3 | 111 | 4 | 2 | 50.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l250_m2_e1 | homalt | 97.8723 | 100.0000 | 95.8333 | 94.0000 | 46 | 0 | 46 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | segdup | * | 99.4321 | 99.1501 | 99.7156 | 94.0254 | 1050 | 9 | 1052 | 3 | 2 | 66.6667 | |
| hfeng-pmm3 | INDEL | I1_5 | segdup | homalt | 99.5772 | 99.5772 | 99.5772 | 92.3820 | 471 | 2 | 471 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | * | hetalt | 96.4340 | 93.1353 | 99.9750 | 38.6184 | 7964 | 587 | 8004 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | I6_15 | map_siren | homalt | 97.7778 | 97.7778 | 97.7778 | 83.4254 | 88 | 2 | 88 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8513 | 99.7206 | 99.9825 | 55.1444 | 17129 | 48 | 17126 | 3 | 2 | 66.6667 | |
| hfeng-pmm3 | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9671 | 99.9671 | 99.9671 | 54.5909 | 6086 | 2 | 6086 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | SNP | * | map_l150_m0_e0 | het | 98.9660 | 98.8665 | 99.0658 | 81.0107 | 7850 | 90 | 7847 | 74 | 2 | 2.7027 | |
| hfeng-pmm3 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.8787 | 99.7922 | 99.9653 | 69.1476 | 11528 | 24 | 11528 | 4 | 2 | 50.0000 | |
| hfeng-pmm3 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.8787 | 99.7922 | 99.9653 | 69.1476 | 11528 | 24 | 11528 | 4 | 2 | 50.0000 | |
| hfeng-pmm3 | SNP | ti | map_l150_m0_e0 | het | 99.0183 | 98.9602 | 99.0764 | 81.1323 | 5044 | 53 | 5042 | 47 | 2 | 4.2553 | |
| hfeng-pmm3 | SNP | ti | map_l250_m0_e0 | homalt | 99.0847 | 99.3119 | 98.8584 | 92.1463 | 433 | 3 | 433 | 5 | 2 | 40.0000 | |
| hfeng-pmm3 | SNP | ti | map_l250_m1_e0 | homalt | 99.5025 | 99.5644 | 99.4406 | 86.8266 | 1600 | 7 | 1600 | 9 | 2 | 22.2222 | |
| hfeng-pmm3 | SNP | ti | map_l250_m2_e0 | homalt | 99.5429 | 99.5998 | 99.4860 | 87.7295 | 1742 | 7 | 1742 | 9 | 2 | 22.2222 | |
| hfeng-pmm3 | SNP | ti | map_l250_m2_e1 | homalt | 99.5488 | 99.6050 | 99.4927 | 87.7689 | 1765 | 7 | 1765 | 9 | 2 | 22.2222 | |
| hfeng-pmm3 | SNP | tv | HG002compoundhet | het | 94.3711 | 89.5142 | 99.7852 | 53.0848 | 4183 | 490 | 4181 | 9 | 2 | 22.2222 | |
| hfeng-pmm3 | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.4812 | 99.0741 | 99.8917 | 37.3686 | 7383 | 69 | 7380 | 8 | 2 | 25.0000 | |
| hfeng-pmm3 | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.9456 | 99.9637 | 99.9275 | 37.1096 | 2757 | 1 | 2757 | 2 | 2 | 100.0000 | |
| 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 | * | map_l125_m0_e0 | het | 90.1770 | 97.4446 | 83.9181 | 93.0825 | 572 | 15 | 574 | 110 | 2 | 1.8182 | |
| jlack-gatk | INDEL | * | map_l150_m0_e0 | homalt | 98.7805 | 98.7805 | 98.7805 | 90.9542 | 162 | 2 | 162 | 2 | 2 | 100.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 95.5259 | 96.5174 | 94.5545 | 88.5617 | 194 | 7 | 191 | 11 | 2 | 18.1818 | |