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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
49851-49900 / 86044 show all | |||||||||||||||
| gduggal-snapfb | SNP | ti | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 62.6263 | 88.5714 | 48.4375 | 94.7840 | 31 | 4 | 31 | 33 | 6 | 18.1818 | |
| hfeng-pmm2 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 93.6381 | 88.5802 | 99.3086 | 86.9266 | 1148 | 148 | 1149 | 8 | 0 | 0.0000 | |
| ciseli-custom | INDEL | D16_PLUS | HG002complexvar | homalt | 50.2549 | 88.5813 | 35.0778 | 60.5689 | 256 | 33 | 248 | 459 | 398 | 86.7102 | |
| ckim-isaac | INDEL | * | HG002complexvar | homalt | 93.1685 | 88.5818 | 98.2561 | 47.1228 | 23941 | 3086 | 23890 | 424 | 132 | 31.1321 | |
| ciseli-custom | INDEL | * | * | homalt | 84.6742 | 88.5829 | 81.0959 | 56.4739 | 110881 | 14291 | 110644 | 25792 | 22639 | 87.7753 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 64.6970 | 88.5882 | 50.9550 | 49.1325 | 753 | 97 | 747 | 719 | 658 | 91.5160 | |
| asubramanian-gatk | INDEL | I6_15 | map_l100_m1_e0 | * | 93.1123 | 88.5965 | 98.1132 | 89.0383 | 101 | 13 | 104 | 2 | 1 | 50.0000 | |
| jpowers-varprowl | INDEL | I1_5 | map_l250_m2_e1 | * | 90.5830 | 88.5965 | 92.6606 | 96.5053 | 101 | 13 | 101 | 8 | 4 | 50.0000 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 91.7140 | 88.5981 | 95.0570 | 53.8425 | 38394 | 4941 | 44230 | 2300 | 2147 | 93.3478 | |
| anovak-vg | SNP | ti | map_l100_m2_e0 | * | 84.5385 | 88.5991 | 80.8339 | 70.4808 | 43379 | 5582 | 43002 | 10196 | 2298 | 22.5383 | |
| gduggal-snapfb | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 17.3977 | 88.6010 | 9.6459 | 80.7136 | 342 | 44 | 365 | 3419 | 49 | 1.4332 | |
| asubramanian-gatk | INDEL | D1_5 | map_l125_m1_e0 | * | 91.7244 | 88.6029 | 95.0739 | 89.7371 | 964 | 124 | 965 | 50 | 5 | 10.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 93.8029 | 88.6076 | 99.6454 | 70.1903 | 280 | 36 | 281 | 1 | 1 | 100.0000 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 92.6603 | 88.6076 | 97.1014 | 74.9319 | 280 | 36 | 268 | 8 | 7 | 87.5000 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 93.7749 | 88.6135 | 99.5748 | 31.3084 | 1144 | 147 | 1171 | 5 | 5 | 100.0000 | |
| ciseli-custom | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 78.0779 | 88.6152 | 69.7802 | 44.4557 | 1907 | 245 | 1905 | 825 | 723 | 87.6364 | |
| gduggal-bwavard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 87.0247 | 88.6166 | 85.4890 | 87.6172 | 1121 | 144 | 1084 | 184 | 65 | 35.3261 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.6448 | 88.6228 | 97.0492 | 64.9425 | 888 | 114 | 888 | 27 | 24 | 88.8889 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 92.7900 | 88.6228 | 97.3684 | 64.6649 | 888 | 114 | 888 | 24 | 21 | 87.5000 | |
| asubramanian-gatk | INDEL | D1_5 | map_l125_m2_e0 | * | 91.8425 | 88.6264 | 95.3008 | 90.1645 | 1013 | 130 | 1014 | 50 | 5 | 10.0000 | |
| ghariani-varprowl | INDEL | I1_5 | * | * | 89.9389 | 88.6296 | 91.2876 | 58.9415 | 133532 | 17131 | 133404 | 12732 | 11050 | 86.7892 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 61.9377 | 88.6347 | 47.6003 | 71.2150 | 1201 | 154 | 1210 | 1332 | 1313 | 98.5736 | |
| ltrigg-rtg1 | SNP | tv | map_l250_m0_e0 | het | 93.8017 | 88.6364 | 99.6063 | 81.4936 | 507 | 65 | 506 | 2 | 0 | 0.0000 | |
| ltrigg-rtg1 | INDEL | I1_5 | map_l100_m1_e0 | hetalt | 92.9362 | 88.6364 | 97.6744 | 92.8808 | 39 | 5 | 42 | 1 | 1 | 100.0000 | |
| ltrigg-rtg1 | INDEL | I1_5 | map_l100_m2_e0 | hetalt | 92.9362 | 88.6364 | 97.6744 | 93.3846 | 39 | 5 | 42 | 1 | 1 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | map_l100_m1_e0 | hetalt | 93.9759 | 88.6364 | 100.0000 | 93.3227 | 39 | 5 | 42 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | I1_5 | map_l100_m2_e0 | hetalt | 93.9759 | 88.6364 | 100.0000 | 93.8053 | 39 | 5 | 42 | 0 | 0 | ||
| jmaeng-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 93.9759 | 88.6364 | 100.0000 | 97.0787 | 39 | 5 | 39 | 0 | 0 | ||
| anovak-vg | INDEL | I1_5 | map_l250_m1_e0 | homalt | 69.3408 | 88.6364 | 56.9444 | 94.4573 | 39 | 5 | 41 | 31 | 28 | 90.3226 | |
| gduggal-bwaplat | SNP | ti | tech_badpromoters | het | 92.8571 | 88.6364 | 97.5000 | 65.2174 | 39 | 5 | 39 | 1 | 0 | 0.0000 | |
| rpoplin-dv42 | INDEL | * | map_l100_m2_e1 | hetalt | 92.8571 | 88.6364 | 97.5000 | 88.9807 | 117 | 15 | 117 | 3 | 0 | 0.0000 | |
| hfeng-pmm2 | INDEL | * | map_l100_m2_e1 | hetalt | 93.9759 | 88.6364 | 100.0000 | 88.0522 | 117 | 15 | 119 | 0 | 0 | ||
| gduggal-snapvard | SNP | ti | tech_badpromoters | het | 91.7647 | 88.6364 | 95.1220 | 57.2917 | 39 | 5 | 39 | 2 | 1 | 50.0000 | |
| gduggal-snapvard | INDEL | I1_5 | map_l250_m1_e0 | homalt | 92.3386 | 88.6364 | 96.3636 | 92.4554 | 39 | 5 | 53 | 2 | 1 | 50.0000 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 89.7154 | 88.6381 | 90.8193 | 44.6755 | 5968 | 765 | 9932 | 1004 | 991 | 98.7052 | |
| anovak-vg | SNP | ti | map_l100_m2_e1 | * | 84.6108 | 88.6390 | 80.9329 | 70.4744 | 43863 | 5622 | 43482 | 10244 | 2310 | 22.5498 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 90.5721 | 88.6430 | 92.5871 | 36.0947 | 21753 | 2787 | 21720 | 1739 | 1695 | 97.4698 | |
| gduggal-bwavard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 93.7898 | 88.6447 | 99.5690 | 61.2364 | 484 | 62 | 462 | 2 | 2 | 100.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 92.3613 | 88.6473 | 96.4000 | 70.3264 | 367 | 47 | 482 | 18 | 17 | 94.4444 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 93.1550 | 88.6524 | 98.1395 | 56.7404 | 6039 | 773 | 844 | 16 | 16 | 100.0000 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 82.3222 | 88.6547 | 76.8340 | 52.5393 | 1430 | 183 | 1393 | 420 | 417 | 99.2857 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 44.3050 | 88.6576 | 29.5314 | 54.8186 | 852 | 109 | 857 | 2045 | 2032 | 99.3643 | |
| jli-custom | INDEL | D16_PLUS | map_l100_m2_e1 | * | 90.5263 | 88.6598 | 92.4731 | 93.0337 | 86 | 11 | 86 | 7 | 2 | 28.5714 | |
| cchapple-custom | INDEL | * | map_siren | hetalt | 0.0000 | 88.6640 | 0.0000 | 0.0000 | 219 | 28 | 0 | 0 | 0 | ||
| mlin-fermikit | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 86.9863 | 88.6640 | 85.3710 | 87.2287 | 2409 | 308 | 2416 | 414 | 264 | 63.7681 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 86.6593 | 88.6640 | 84.7432 | 65.8939 | 219 | 28 | 561 | 101 | 76 | 75.2475 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 93.3698 | 88.6709 | 98.5945 | 70.7743 | 1401 | 179 | 1403 | 20 | 6 | 30.0000 | |
| rpoplin-dv42 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 93.8172 | 88.6758 | 99.5914 | 32.3428 | 1942 | 248 | 1950 | 8 | 8 | 100.0000 | |
| asubramanian-gatk | INDEL | D1_5 | map_l125_m2_e1 | * | 91.8963 | 88.6776 | 95.3575 | 90.2011 | 1026 | 131 | 1027 | 50 | 5 | 10.0000 | |
| asubramanian-gatk | INDEL | * | map_l250_m0_e0 | het | 80.3419 | 88.6792 | 73.4375 | 98.2773 | 47 | 6 | 47 | 17 | 1 | 5.8824 | |