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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
9151-9200 / 86044 show all | |||||||||||||||
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 63.1989 | 46.4849 | 98.6799 | 45.9893 | 324 | 373 | 299 | 4 | 4 | 100.0000 | |
| ckim-isaac | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 94.2905 | 92.1704 | 96.5104 | 61.7853 | 4391 | 373 | 4425 | 160 | 47 | 29.3750 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.5950 | 86.3019 | 99.8782 | 37.9441 | 2350 | 373 | 2460 | 3 | 3 | 100.0000 | |
| ndellapenna-hhga | SNP | ti | map_l125_m2_e0 | het | 98.8804 | 98.0239 | 99.7520 | 70.6633 | 18503 | 373 | 18503 | 46 | 20 | 43.4783 | |
| ltrigg-rtg2 | SNP | tv | map_siren | het | 99.1276 | 98.6962 | 99.5628 | 47.7162 | 28236 | 373 | 28241 | 124 | 4 | 3.2258 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 93.7450 | 89.4498 | 98.4735 | 43.0447 | 3154 | 372 | 3161 | 49 | 44 | 89.7959 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 93.7450 | 89.4498 | 98.4735 | 43.0447 | 3154 | 372 | 3161 | 49 | 44 | 89.7959 | |
| mlin-fermikit | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 79.3723 | 90.3851 | 70.7516 | 51.9765 | 3497 | 372 | 3464 | 1432 | 1427 | 99.6508 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 94.6431 | 90.7255 | 98.9142 | 65.3727 | 3639 | 372 | 3644 | 40 | 7 | 17.5000 | |
| jli-custom | INDEL | D6_15 | HG002compoundhet | * | 96.8618 | 95.8809 | 97.8630 | 33.8766 | 8659 | 372 | 8655 | 189 | 186 | 98.4127 | |
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 92.4949 | 86.3386 | 99.5964 | 37.6133 | 2351 | 372 | 2468 | 10 | 10 | 100.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.8875 | 94.6157 | 99.2711 | 52.0847 | 6537 | 372 | 6537 | 48 | 43 | 89.5833 | |
| gduggal-snapvard | SNP | ti | map_l100_m0_e0 | homalt | 97.3605 | 95.2148 | 99.6052 | 63.3538 | 7402 | 372 | 7316 | 29 | 23 | 79.3103 | |
| gduggal-snapvard | SNP | tv | map_l150_m1_e0 | * | 91.4337 | 96.5909 | 86.7993 | 81.5080 | 10540 | 372 | 10514 | 1599 | 100 | 6.2539 | |
| jlack-gatk | SNP | ti | HG002complexvar | het | 99.8980 | 99.8818 | 99.9142 | 17.5660 | 314394 | 372 | 314340 | 270 | 88 | 32.5926 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.5311 | 96.0668 | 99.0408 | 42.6732 | 9086 | 372 | 9086 | 88 | 81 | 92.0455 | |
| dgrover-gatk | SNP | ti | HG002complexvar | * | 99.9530 | 99.9268 | 99.9791 | 17.5262 | 508064 | 372 | 508000 | 106 | 56 | 52.8302 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.9180 | 98.7044 | 99.1325 | 79.1132 | 28340 | 372 | 28340 | 248 | 29 | 11.6935 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.9180 | 98.7044 | 99.1325 | 79.1132 | 28340 | 372 | 28340 | 248 | 29 | 11.6935 | |
| egarrison-hhga | SNP | * | map_l125_m2_e0 | het | 99.2355 | 98.7312 | 99.7450 | 71.3586 | 28946 | 372 | 28946 | 74 | 28 | 37.8378 | |
| ckim-isaac | INDEL | D1_5 | map_l125_m1_e0 | * | 78.8546 | 65.8088 | 98.3516 | 87.2415 | 716 | 372 | 716 | 12 | 6 | 50.0000 | |
| ckim-isaac | INDEL | I6_15 | HG002complexvar | homalt | 79.2387 | 69.4399 | 92.2574 | 47.0554 | 843 | 371 | 846 | 71 | 37 | 52.1127 | |
| gduggal-bwaplat | INDEL | I16_PLUS | HG002complexvar | het | 60.5561 | 44.2105 | 96.0784 | 72.5561 | 294 | 371 | 294 | 12 | 5 | 41.6667 | |
| gduggal-bwafb | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 96.6527 | 94.4759 | 98.9323 | 48.2177 | 6345 | 371 | 7042 | 76 | 21 | 27.6316 | |
| ndellapenna-hhga | SNP | ti | map_l100_m0_e0 | * | 99.0443 | 98.2959 | 99.8041 | 65.3402 | 21400 | 371 | 21401 | 42 | 25 | 59.5238 | |
| ndellapenna-hhga | SNP | ti | map_l125_m1_e0 | het | 98.8592 | 97.9689 | 99.7658 | 69.2090 | 17895 | 371 | 17895 | 42 | 20 | 47.6190 | |
| cchapple-custom | SNP | ti | map_l125_m1_e0 | homalt | 98.2873 | 96.6410 | 99.9906 | 60.9405 | 10674 | 371 | 10672 | 1 | 1 | 100.0000 | |
| ckim-dragen | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.0246 | 94.5657 | 99.6148 | 24.0847 | 6456 | 371 | 6465 | 25 | 25 | 100.0000 | |
| gduggal-snapplat | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 96.7832 | 94.0810 | 99.6452 | 50.9082 | 5897 | 371 | 5898 | 21 | 4 | 19.0476 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | * | 49.6345 | 46.9154 | 52.6882 | 51.2725 | 327 | 370 | 343 | 308 | 167 | 54.2208 | |
| gduggal-snapplat | INDEL | D1_5 | map_l100_m1_e0 | * | 85.3263 | 79.9784 | 91.4407 | 90.7363 | 1478 | 370 | 1720 | 161 | 32 | 19.8758 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 4.6004 | 2.3747 | 73.3333 | 89.3617 | 9 | 370 | 11 | 4 | 2 | 50.0000 | |
| gduggal-bwafb | SNP | * | map_l125_m2_e0 | het | 98.4559 | 98.7380 | 98.1754 | 76.1231 | 28948 | 370 | 28948 | 538 | 123 | 22.8625 | |
| gduggal-bwafb | SNP | * | map_l125_m2_e1 | het | 98.4726 | 98.7517 | 98.1951 | 76.1869 | 29270 | 370 | 29270 | 538 | 123 | 22.8625 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 69.2265 | 56.5217 | 89.2989 | 95.0257 | 481 | 370 | 484 | 58 | 10 | 17.2414 | |
| egarrison-hhga | INDEL | I16_PLUS | HG002compoundhet | * | 86.9177 | 82.7345 | 91.5464 | 49.7800 | 1773 | 370 | 1776 | 164 | 118 | 71.9512 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 45.6818 | 35.2014 | 65.0485 | 65.2418 | 201 | 370 | 201 | 108 | 80 | 74.0741 | |
| jpowers-varprowl | SNP | ti | map_l150_m0_e0 | * | 96.1494 | 95.2932 | 97.0211 | 84.0052 | 7491 | 370 | 7491 | 230 | 86 | 37.3913 | |
| ltrigg-rtg1 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.8166 | 98.1371 | 99.5056 | 55.0392 | 19492 | 370 | 19523 | 97 | 32 | 32.9897 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 75.2854 | 64.8571 | 89.7098 | 61.7172 | 681 | 369 | 680 | 78 | 71 | 91.0256 | |
| jpowers-varprowl | INDEL | * | map_l100_m1_e0 | * | 91.2993 | 89.7100 | 92.9459 | 84.6574 | 3217 | 369 | 3215 | 244 | 196 | 80.3279 | |
| jmaeng-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 84.2444 | 82.4369 | 86.1329 | 57.6838 | 1732 | 369 | 1646 | 265 | 260 | 98.1132 | |
| ckim-isaac | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 92.5831 | 88.2783 | 97.3293 | 62.2126 | 2779 | 369 | 2879 | 79 | 3 | 3.7975 | |
| raldana-dualsentieon | SNP | * | map_l100_m2_e0 | het | 99.0893 | 99.2047 | 98.9741 | 68.2725 | 46030 | 369 | 46019 | 477 | 7 | 1.4675 | |
| raldana-dualsentieon | SNP | * | map_l100_m2_e1 | het | 99.0916 | 99.2132 | 98.9703 | 68.3138 | 46529 | 369 | 46518 | 484 | 7 | 1.4463 | |
| ndellapenna-hhga | INDEL | I16_PLUS | * | hetalt | 89.6769 | 82.4118 | 98.3466 | 51.6538 | 1729 | 369 | 1725 | 29 | 24 | 82.7586 | |
| ndellapenna-hhga | INDEL | I16_PLUS | HG002compoundhet | hetalt | 90.0250 | 82.3698 | 99.2490 | 40.2898 | 1724 | 369 | 1718 | 13 | 9 | 69.2308 | |
| ltrigg-rtg2 | SNP | ti | map_l125_m0_e0 | het | 97.6557 | 95.5343 | 99.8735 | 55.0552 | 7894 | 369 | 7894 | 10 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5995 | 98.7927 | 98.4071 | 74.5792 | 30112 | 368 | 29653 | 480 | 385 | 80.2083 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.5995 | 98.7927 | 98.4071 | 74.5792 | 30112 | 368 | 29653 | 480 | 385 | 80.2083 | |