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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
66251-66300 / 86044 show all | |||||||||||||||
| eyeh-varpipe | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 53.8085 | 55.7377 | 52.0085 | 38.7306 | 68 | 54 | 246 | 227 | 226 | 99.5595 | |
| gduggal-bwavard | INDEL | I6_15 | HG002compoundhet | het | 6.3867 | 74.0385 | 3.3373 | 37.4814 | 154 | 54 | 168 | 4866 | 4788 | 98.3970 | |
| gduggal-bwavard | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 66.5015 | 91.0448 | 52.3810 | 62.2662 | 549 | 54 | 539 | 490 | 476 | 97.1429 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 98.7414 | 97.6021 | 99.9075 | 50.0923 | 2198 | 54 | 2161 | 2 | 0 | 0.0000 | |
| gduggal-snapfb | INDEL | * | func_cds | * | 91.5789 | 87.8652 | 95.6204 | 38.2883 | 391 | 54 | 393 | 18 | 12 | 66.6667 | |
| eyeh-varpipe | SNP | * | HG002compoundhet | homalt | 97.1233 | 99.4992 | 94.8583 | 47.6589 | 10728 | 54 | 3616 | 196 | 81 | 41.3265 | |
| eyeh-varpipe | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.0524 | 98.8880 | 95.2837 | 61.3406 | 4802 | 54 | 4182 | 207 | 43 | 20.7729 | |
| gduggal-bwafb | INDEL | * | map_l100_m2_e1 | hetalt | 73.5849 | 59.0909 | 97.5000 | 93.2660 | 78 | 54 | 39 | 1 | 1 | 100.0000 | |
| gduggal-bwafb | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.5168 | 98.8880 | 96.1831 | 70.9711 | 4802 | 54 | 4813 | 191 | 46 | 24.0838 | |
| gduggal-bwafb | SNP | tv | map_l125_m2_e0 | homalt | 99.4828 | 99.1025 | 99.8660 | 70.9836 | 5963 | 54 | 5963 | 8 | 6 | 75.0000 | |
| gduggal-bwafb | SNP | tv | map_l125_m2_e1 | homalt | 99.4877 | 99.1110 | 99.8673 | 71.0512 | 6020 | 54 | 6020 | 8 | 6 | 75.0000 | |
| gduggal-bwafb | SNP | tv | segdup | * | 98.7191 | 99.3671 | 98.0796 | 93.0076 | 8478 | 54 | 8478 | 166 | 14 | 8.4337 | |
| gduggal-bwaplat | INDEL | * | func_cds | * | 93.3174 | 87.8652 | 99.4911 | 51.1194 | 391 | 54 | 391 | 2 | 2 | 100.0000 | |
| gduggal-bwaplat | INDEL | * | map_l250_m0_e0 | * | 47.0588 | 30.7692 | 100.0000 | 99.5667 | 24 | 54 | 24 | 0 | 0 | ||
| gduggal-bwaplat | INDEL | D16_PLUS | map_l100_m2_e1 | * | 60.9929 | 44.3299 | 97.7273 | 95.8015 | 43 | 54 | 43 | 1 | 1 | 100.0000 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.5323 | 99.5000 | 99.5646 | 79.8322 | 10747 | 54 | 10747 | 47 | 15 | 31.9149 | |
| dgrover-gatk | SNP | tv | map_l250_m1_e0 | * | 98.0711 | 97.9600 | 98.1825 | 89.6431 | 2593 | 54 | 2593 | 48 | 11 | 22.9167 | |
| ckim-isaac | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 98.0365 | 96.2158 | 99.9273 | 21.3265 | 1373 | 54 | 1375 | 1 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 87.8228 | 89.7533 | 85.9736 | 75.4953 | 473 | 54 | 521 | 85 | 78 | 91.7647 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 93.3540 | 87.6993 | 99.7881 | 34.6260 | 385 | 54 | 471 | 1 | 1 | 100.0000 | |
| egarrison-hhga | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 98.6867 | 98.3374 | 99.0385 | 67.1791 | 3194 | 54 | 3193 | 31 | 11 | 35.4839 | |
| eyeh-varpipe | INDEL | * | map_l150_m2_e0 | * | 96.5842 | 96.1648 | 97.0072 | 95.5563 | 1354 | 54 | 1880 | 58 | 41 | 70.6897 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.6983 | 97.4954 | 97.9021 | 76.6822 | 2102 | 54 | 2100 | 45 | 20 | 44.4444 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | * | 92.6612 | 92.6531 | 92.6694 | 58.4244 | 681 | 54 | 670 | 53 | 51 | 96.2264 | |
| ckim-isaac | INDEL | D6_15 | map_l150_m2_e1 | * | 52.9915 | 36.4706 | 96.8750 | 93.7864 | 31 | 54 | 31 | 1 | 1 | 100.0000 | |
| hfeng-pmm1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 88.4462 | 80.4348 | 98.2301 | 90.4922 | 222 | 54 | 222 | 4 | 0 | 0.0000 | |
| hfeng-pmm1 | SNP | ti | map_l250_m2_e1 | * | 99.0337 | 98.9362 | 99.1315 | 88.6771 | 5022 | 54 | 5022 | 44 | 10 | 22.7273 | |
| hfeng-pmm1 | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 98.0879 | 96.4380 | 99.7952 | 66.9971 | 1462 | 54 | 1462 | 3 | 1 | 33.3333 | |
| hfeng-pmm3 | SNP | tv | map_l100_m0_e0 | het | 99.3072 | 99.2523 | 99.3623 | 70.7621 | 7168 | 54 | 7167 | 46 | 4 | 8.6957 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.8132 | 94.2797 | 99.4867 | 30.0790 | 890 | 54 | 969 | 5 | 5 | 100.0000 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.5817 | 91.8058 | 99.6815 | 70.4887 | 605 | 54 | 626 | 2 | 1 | 50.0000 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.5817 | 91.8058 | 99.6815 | 70.4887 | 605 | 54 | 626 | 2 | 1 | 50.0000 | |
| jlack-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.0016 | 98.8665 | 99.1370 | 66.6503 | 4710 | 54 | 4710 | 41 | 9 | 21.9512 | |
| jlack-gatk | SNP | ti | map_l250_m2_e1 | het | 92.2399 | 98.3631 | 86.8344 | 94.0808 | 3245 | 54 | 3245 | 492 | 42 | 8.5366 | |
| ckim-dragen | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.9650 | 99.8245 | 98.1202 | 75.4285 | 30707 | 54 | 30692 | 588 | 582 | 98.9796 | |
| ciseli-custom | INDEL | D6_15 | map_l125_m1_e0 | * | 54.5455 | 53.8462 | 55.2632 | 91.9718 | 63 | 54 | 63 | 51 | 28 | 54.9020 | |
| ckim-gatk | SNP | tv | segdup | * | 98.7820 | 99.3671 | 98.2037 | 94.6419 | 8478 | 54 | 8474 | 155 | 6 | 3.8710 | |
| ckim-isaac | INDEL | * | segdup | het | 97.0051 | 96.3165 | 97.7035 | 93.8034 | 1412 | 54 | 1404 | 33 | 20 | 60.6061 | |
| ckim-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 93.3540 | 87.6993 | 99.7881 | 34.6260 | 385 | 54 | 471 | 1 | 1 | 100.0000 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.9393 | 99.0763 | 96.8281 | 71.9883 | 5792 | 54 | 5739 | 188 | 172 | 91.4894 | |
| ckim-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.9393 | 99.0763 | 96.8281 | 71.9883 | 5792 | 54 | 5739 | 188 | 172 | 91.4894 | |
| cchapple-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.6415 | 96.0148 | 97.2764 | 66.3029 | 1301 | 54 | 2643 | 74 | 62 | 83.7838 | |
| cchapple-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.2823 | 95.8333 | 98.7758 | 84.0415 | 1242 | 54 | 1291 | 16 | 13 | 81.2500 | |
| gduggal-snapvard | SNP | tv | map_l250_m1_e0 | homalt | 96.5675 | 93.6916 | 99.6255 | 87.3500 | 802 | 54 | 798 | 3 | 2 | 66.6667 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 0.0000 | 1.8182 | 0.0000 | 0.0000 | 1 | 54 | 0 | 0 | 0 | ||
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 34.5747 | 92.5000 | 21.2608 | 78.3172 | 666 | 54 | 715 | 2648 | 56 | 2.1148 | |
| ghariani-varprowl | SNP | ti | map_l250_m1_e0 | homalt | 98.1979 | 96.6397 | 99.8072 | 87.4354 | 1553 | 54 | 1553 | 3 | 3 | 100.0000 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 18.8667 | 23.9437 | 15.5660 | 65.0165 | 17 | 54 | 33 | 179 | 132 | 73.7430 | |
| gduggal-snapplat | INDEL | I6_15 | map_l100_m2_e0 | het | 17.8344 | 11.4754 | 40.0000 | 94.1406 | 7 | 54 | 6 | 9 | 0 | 0.0000 | |
| gduggal-snapplat | INDEL | I6_15 | map_l100_m2_e1 | het | 17.8344 | 11.4754 | 40.0000 | 94.2748 | 7 | 54 | 6 | 9 | 0 | 0.0000 | |