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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
8151-8200 / 86044 show all | |||||||||||||||
| asubramanian-gatk | INDEL | C6_15 | * | * | 0.0000 | 100.0000 | 0.0000 | 80.1262 | 7 | 0 | 0 | 189 | 0 | 0.0000 | |
| bgallagher-sentieon | SNP | ti | map_l100_m0_e0 | het | 98.9661 | 99.2777 | 98.6565 | 72.6282 | 13882 | 101 | 13879 | 189 | 28 | 14.8148 | |
| bgallagher-sentieon | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 97.9485 | 99.8507 | 96.1175 | 40.3651 | 4682 | 7 | 4679 | 189 | 1 | 0.5291 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 32.6491 | 36.5854 | 29.4776 | 59.7598 | 75 | 130 | 79 | 189 | 100 | 52.9101 | |
| anovak-vg | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 32.6491 | 36.5854 | 29.4776 | 59.7598 | 75 | 130 | 79 | 189 | 100 | 52.9101 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.2882 | 97.8105 | 96.7714 | 71.7102 | 5718 | 128 | 5665 | 189 | 174 | 92.0635 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.2882 | 97.8105 | 96.7714 | 71.7102 | 5718 | 128 | 5665 | 189 | 174 | 92.0635 | |
| jli-custom | INDEL | D6_15 | HG002compoundhet | * | 96.8618 | 95.8809 | 97.8630 | 33.8766 | 8659 | 372 | 8655 | 189 | 186 | 98.4127 | |
| jpowers-varprowl | SNP | * | map_l250_m0_e0 | het | 90.2202 | 92.4967 | 88.0531 | 95.2498 | 1393 | 113 | 1393 | 189 | 29 | 15.3439 | |
| jmaeng-gatk | INDEL | D6_15 | HG002compoundhet | het | 88.9799 | 98.0140 | 81.4706 | 68.2342 | 839 | 17 | 831 | 189 | 187 | 98.9418 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 96.0835 | 99.8396 | 92.5998 | 68.1347 | 2490 | 4 | 2365 | 189 | 7 | 3.7037 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.8975 | 95.7372 | 96.0584 | 69.6019 | 4649 | 207 | 4606 | 189 | 80 | 42.3280 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | het | 94.8865 | 95.8225 | 93.9686 | 74.8872 | 2959 | 129 | 2929 | 188 | 79 | 42.0213 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 96.6942 | 99.6620 | 93.8981 | 67.0587 | 2949 | 10 | 2893 | 188 | 6 | 3.1915 | |
| gduggal-bwafb | INDEL | I1_5 | HG002complexvar | het | 97.6126 | 96.2835 | 98.9789 | 54.8150 | 17513 | 676 | 18224 | 188 | 155 | 82.4468 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 40.3388 | 26.9615 | 80.0636 | 58.9286 | 756 | 2048 | 755 | 188 | 171 | 90.9574 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 95.5538 | 96.9440 | 94.2029 | 48.6379 | 1142 | 36 | 3055 | 188 | 176 | 93.6170 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 89.8601 | 93.0301 | 86.8990 | 65.5793 | 1268 | 95 | 1247 | 188 | 182 | 96.8085 | |
| mlin-fermikit | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 85.3371 | 87.1377 | 83.6094 | 85.7161 | 962 | 142 | 959 | 188 | 129 | 68.6170 | |
| 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 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 98.5480 | 97.7849 | 99.3232 | 55.6830 | 27634 | 626 | 27589 | 188 | 94 | 50.0000 | |
| jpowers-varprowl | SNP | ti | map_l250_m1_e0 | het | 93.7195 | 93.7668 | 93.6722 | 91.9387 | 2783 | 185 | 2783 | 188 | 54 | 28.7234 | |
| jli-custom | SNP | * | map_l125_m1_e0 | het | 99.0623 | 98.7919 | 99.3341 | 68.8001 | 28049 | 343 | 28046 | 188 | 54 | 28.7234 | |
| jli-custom | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.6800 | 99.8524 | 97.5347 | 38.6336 | 7441 | 11 | 7438 | 188 | 3 | 1.5957 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.0126 | 98.9729 | 99.0524 | 59.2954 | 19658 | 204 | 19651 | 188 | 96 | 51.0638 | |
| hfeng-pmm3 | INDEL | I6_15 | HG002compoundhet | homalt | 24.8000 | 100.0000 | 14.1553 | 62.6280 | 31 | 0 | 31 | 188 | 187 | 99.4681 | |
| anovak-vg | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 49.2182 | 39.3273 | 65.7559 | 77.6192 | 304 | 469 | 361 | 188 | 52 | 27.6596 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 98.8291 | 99.8805 | 97.7996 | 55.4001 | 8356 | 10 | 8356 | 188 | 186 | 98.9362 | |
| bgallagher-sentieon | SNP | ti | map_l150_m2_e0 | het | 98.8935 | 99.2392 | 98.5502 | 79.6724 | 12783 | 98 | 12779 | 188 | 30 | 15.9574 | |
| bgallagher-sentieon | SNP | tv | map_l125_m2_e0 | * | 99.1716 | 99.4784 | 98.8667 | 73.4826 | 16403 | 86 | 16401 | 188 | 28 | 14.8936 | |
| bgallagher-sentieon | SNP | tv | map_l125_m2_e1 | * | 99.1800 | 99.4837 | 98.8781 | 73.5318 | 16571 | 86 | 16569 | 188 | 28 | 14.8936 | |
| bgallagher-sentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.1583 | 99.0954 | 95.2956 | 68.4624 | 3834 | 35 | 3788 | 187 | 181 | 96.7914 | |
| bgallagher-sentieon | SNP | tv | map_l125_m1_e0 | * | 99.1503 | 99.4630 | 98.8396 | 71.8727 | 15930 | 86 | 15928 | 187 | 28 | 14.9733 | |
| asubramanian-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.9673 | 98.9982 | 98.9364 | 66.6862 | 17392 | 176 | 17395 | 187 | 18 | 9.6257 | |
| bgallagher-sentieon | INDEL | D6_15 | HG002compoundhet | het | 89.1342 | 98.1308 | 81.6487 | 68.8379 | 840 | 16 | 832 | 187 | 185 | 98.9305 | |
| bgallagher-sentieon | INDEL | D6_15 | HG002compoundhet | homalt | 20.4255 | 100.0000 | 11.3744 | 65.9677 | 24 | 0 | 24 | 187 | 186 | 99.4652 | |
| anovak-vg | SNP | tv | segdup | * | 97.7325 | 97.6676 | 97.7974 | 93.3295 | 8333 | 199 | 8303 | 187 | 80 | 42.7807 | |
| anovak-vg | INDEL | * | map_l150_m2_e1 | homalt | 76.1446 | 84.3496 | 69.3944 | 88.0547 | 415 | 77 | 424 | 187 | 167 | 89.3048 | |
| qzeng-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 96.0217 | 94.2549 | 97.8560 | 49.0716 | 3675 | 224 | 8535 | 187 | 123 | 65.7754 | |
| qzeng-custom | SNP | ti | HG002compoundhet | het | 98.0838 | 97.7380 | 98.4320 | 42.6883 | 9290 | 215 | 11739 | 187 | 45 | 24.0642 | |
| ltrigg-rtg2 | SNP | ti | map_siren | het | 99.2569 | 98.8202 | 99.6976 | 45.2238 | 61645 | 736 | 61646 | 187 | 11 | 5.8824 | |
| gduggal-snapfb | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 50.6602 | 37.5000 | 78.0516 | 49.9118 | 1434 | 2390 | 665 | 187 | 113 | 60.4278 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m2_e1 | * | 92.7581 | 94.9974 | 90.6219 | 86.9648 | 1842 | 97 | 1807 | 187 | 51 | 27.2727 | |
| raldana-dualsentieon | INDEL | D6_15 | HG002compoundhet | het | 78.4773 | 78.8551 | 78.1030 | 69.3467 | 675 | 181 | 667 | 187 | 185 | 98.9305 | |
| gduggal-snapvard | INDEL | D1_5 | map_l125_m0_e0 | het | 81.8658 | 97.6812 | 70.4581 | 90.5282 | 337 | 8 | 446 | 187 | 38 | 20.3209 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | het | 76.6206 | 85.4508 | 69.4444 | 82.3834 | 417 | 71 | 425 | 187 | 171 | 91.4439 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 94.5739 | 94.2717 | 94.8781 | 48.0950 | 3456 | 210 | 3464 | 187 | 150 | 80.2139 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 93.3647 | 97.9109 | 89.2219 | 85.2038 | 1781 | 38 | 1548 | 187 | 133 | 71.1230 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 93.3647 | 97.9109 | 89.2219 | 85.2038 | 1781 | 38 | 1548 | 187 | 133 | 71.1230 | |