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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
8451-8500 / 86044 show all | |||||||||||||||
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 83.3645 | 86.4174 | 80.5198 | 60.1495 | 2774 | 436 | 3005 | 727 | 352 | 48.4182 | |
| ltrigg-rtg2 | SNP | ti | map_l150_m2_e1 | het | 98.2274 | 96.6500 | 99.8571 | 62.1754 | 12579 | 436 | 12581 | 18 | 1 | 5.5556 | |
| ndellapenna-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 74.7342 | 66.9196 | 84.6154 | 62.9705 | 882 | 436 | 924 | 168 | 144 | 85.7143 | |
| gduggal-bwafb | SNP | ti | map_l100_m2_e0 | * | 99.1045 | 99.1095 | 99.0994 | 68.4259 | 48525 | 436 | 48527 | 441 | 108 | 24.4898 | |
| gduggal-bwafb | SNP | ti | map_l100_m2_e1 | * | 99.1089 | 99.1189 | 99.0989 | 68.4487 | 49049 | 436 | 49051 | 446 | 108 | 24.2152 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 76.0853 | 63.1134 | 95.7692 | 72.6027 | 746 | 436 | 747 | 33 | 30 | 90.9091 | |
| gduggal-bwaplat | SNP | tv | map_l250_m0_e0 | het | 38.3099 | 23.7762 | 98.5507 | 99.1755 | 136 | 436 | 136 | 2 | 0 | 0.0000 | |
| gduggal-bwafb | SNP | * | map_l150_m2_e1 | * | 98.6663 | 98.6464 | 98.6862 | 78.1729 | 31774 | 436 | 31774 | 423 | 108 | 25.5319 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.8169 | 93.8695 | 99.9554 | 27.7467 | 6676 | 436 | 6718 | 3 | 2 | 66.6667 | |
| cchapple-custom | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 84.8454 | 79.2480 | 91.2936 | 44.8269 | 1665 | 436 | 2590 | 247 | 237 | 95.9514 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.6969 | 92.8325 | 94.5775 | 63.9536 | 5647 | 436 | 5529 | 317 | 301 | 94.9527 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.9920 | 92.6052 | 99.6360 | 39.6618 | 5460 | 436 | 5475 | 20 | 20 | 100.0000 | |
| rpoplin-dv42 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.9920 | 92.6052 | 99.6360 | 39.6618 | 5460 | 436 | 5475 | 20 | 20 | 100.0000 | |
| egarrison-hhga | INDEL | D1_5 | HG002complexvar | hetalt | 79.1212 | 67.7515 | 95.0766 | 77.6746 | 916 | 436 | 869 | 45 | 42 | 93.3333 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.1530 | 92.6221 | 99.9638 | 35.0611 | 5461 | 435 | 5523 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.1530 | 92.6221 | 99.9638 | 35.0611 | 5461 | 435 | 5523 | 2 | 2 | 100.0000 | |
| eyeh-varpipe | INDEL | * | map_siren | * | 94.7665 | 94.1296 | 95.4122 | 91.1520 | 6975 | 435 | 7882 | 379 | 279 | 73.6148 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.1311 | 92.6743 | 99.8558 | 64.0650 | 5503 | 435 | 5540 | 8 | 7 | 87.5000 | |
| ltrigg-rtg2 | INDEL | I1_5 | * | het | 99.5106 | 99.4497 | 99.5716 | 56.0879 | 78606 | 435 | 77868 | 335 | 92 | 27.4627 | |
| jpowers-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 43.2760 | 32.9738 | 62.9412 | 68.5185 | 214 | 435 | 214 | 126 | 91 | 72.2222 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.3400 | 95.3206 | 99.4468 | 70.6377 | 8861 | 435 | 8988 | 50 | 50 | 100.0000 | |
| gduggal-snapfb | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 0.0000 | 0.2294 | 0.0000 | 0.0000 | 1 | 435 | 0 | 0 | 0 | ||
| gduggal-bwafb | SNP | * | map_l150_m2_e0 | * | 98.6575 | 98.6343 | 98.6808 | 78.1008 | 31417 | 435 | 31417 | 420 | 107 | 25.4762 | |
| eyeh-varpipe | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 48.0410 | 32.1373 | 95.1060 | 47.1096 | 206 | 435 | 583 | 30 | 30 | 100.0000 | |
| gduggal-bwavard | SNP | * | map_l125_m2_e0 | homalt | 98.6652 | 97.4964 | 99.8623 | 68.6081 | 16940 | 435 | 16685 | 23 | 18 | 78.2609 | |
| gduggal-bwavard | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.2565 | 97.5239 | 96.9905 | 69.1218 | 17133 | 435 | 16952 | 526 | 189 | 35.9316 | |
| rpoplin-dv42 | SNP | * | map_l125_m2_e1 | * | 99.2571 | 99.0784 | 99.4365 | 70.8435 | 46767 | 435 | 46761 | 265 | 170 | 64.1509 | |
| rpoplin-dv42 | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 98.4674 | 99.0988 | 97.8440 | 74.2336 | 47836 | 435 | 47787 | 1053 | 987 | 93.7322 | |
| rpoplin-dv42 | INDEL | D16_PLUS | * | * | 94.4399 | 93.5879 | 95.3076 | 64.2354 | 6349 | 435 | 6337 | 312 | 290 | 92.9487 | |
| cchapple-custom | SNP | tv | * | homalt | 99.9396 | 99.8847 | 99.9947 | 18.4432 | 376688 | 435 | 376084 | 20 | 17 | 85.0000 | |
| cchapple-custom | SNP | tv | map_l125_m2_e0 | * | 96.6110 | 97.3619 | 95.8717 | 75.9113 | 16054 | 435 | 16047 | 691 | 117 | 16.9320 | |
| cchapple-custom | SNP | tv | map_l125_m2_e1 | * | 96.6306 | 97.3885 | 95.8843 | 75.9688 | 16222 | 435 | 16215 | 696 | 117 | 16.8103 | |
| cchapple-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 0.0000 | 93.8836 | 0.0000 | 0.0000 | 6677 | 435 | 0 | 0 | 0 | ||
| ciseli-custom | INDEL | D1_5 | map_siren | het | 83.5161 | 80.9398 | 86.2617 | 86.1336 | 1843 | 434 | 1846 | 294 | 66 | 22.4490 | |
| gduggal-snapplat | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 78.2077 | 80.0368 | 76.4603 | 79.5968 | 1740 | 434 | 1741 | 536 | 6 | 1.1194 | |
| ltrigg-rtg2 | SNP | ti | map_l150_m2_e0 | het | 98.2167 | 96.6307 | 99.8556 | 61.9797 | 12447 | 434 | 12450 | 18 | 1 | 5.5556 | |
| qzeng-custom | INDEL | D16_PLUS | HG002compoundhet | * | 75.9486 | 81.4609 | 71.1351 | 32.7367 | 1907 | 434 | 2112 | 857 | 326 | 38.0397 | |
| jlack-gatk | SNP | ti | map_l100_m1_e0 | * | 97.4794 | 99.0945 | 95.9161 | 72.9428 | 47497 | 434 | 47490 | 2022 | 193 | 9.5450 | |
| ltrigg-rtg1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.8306 | 94.1224 | 99.6991 | 48.9729 | 6950 | 434 | 6959 | 21 | 10 | 47.6190 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.3971 | 97.0646 | 97.7319 | 53.7356 | 14351 | 434 | 14349 | 333 | 323 | 96.9970 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 91.1773 | 86.7440 | 96.0881 | 48.8639 | 2840 | 434 | 2530 | 103 | 98 | 95.1456 | |
| eyeh-varpipe | INDEL | D1_5 | * | homalt | 95.4519 | 99.1150 | 92.0499 | 59.2107 | 48493 | 433 | 48444 | 4184 | 4111 | 98.2553 | |
| gduggal-bwaplat | INDEL | D6_15 | HG002compoundhet | het | 62.5277 | 49.4159 | 85.1107 | 78.7243 | 423 | 433 | 423 | 74 | 34 | 45.9459 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 97.6101 | 95.3421 | 99.9887 | 62.3644 | 8863 | 433 | 8881 | 1 | 0 | 0.0000 | |
| gduggal-snapvard | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 57.3545 | 40.9277 | 95.8084 | 61.2079 | 300 | 433 | 320 | 14 | 12 | 85.7143 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 73.7913 | 59.3427 | 97.5400 | 44.2387 | 632 | 433 | 793 | 20 | 13 | 65.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 97.0680 | 94.6510 | 99.6117 | 25.8826 | 7662 | 433 | 7696 | 30 | 29 | 96.6667 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.1910 | 92.7080 | 99.9459 | 61.2682 | 5505 | 433 | 5543 | 3 | 3 | 100.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.1713 | 92.6560 | 99.9638 | 35.0529 | 5463 | 433 | 5525 | 2 | 2 | 100.0000 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.1713 | 92.6560 | 99.9638 | 35.0529 | 5463 | 433 | 5525 | 2 | 2 | 100.0000 | |