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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
7801-7850 / 86044 show all | |||||||||||||||
| gduggal-snapvard | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 88.6909 | 97.1990 | 81.5523 | 71.2536 | 17351 | 500 | 17263 | 3905 | 147 | 3.7644 | |
| anovak-vg | INDEL | D16_PLUS | HG002complexvar | het | 65.7371 | 54.8329 | 82.0546 | 48.1457 | 607 | 500 | 631 | 138 | 95 | 68.8406 | |
| eyeh-varpipe | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 62.1754 | 45.8288 | 96.6488 | 62.3613 | 423 | 500 | 721 | 25 | 23 | 92.0000 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.7692 | 97.9625 | 99.5893 | 34.5018 | 24040 | 500 | 24005 | 99 | 66 | 66.6667 | |
| ltrigg-rtg2 | SNP | ti | map_l125_m2_e1 | het | 98.5813 | 97.3804 | 99.8121 | 58.3672 | 18587 | 500 | 18589 | 35 | 4 | 11.4286 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.8385 | 93.8823 | 99.9870 | 28.1495 | 7673 | 500 | 7710 | 1 | 0 | 0.0000 | |
| gduggal-bwavard | SNP | ti | map_l150_m2_e0 | * | 95.3841 | 97.5624 | 93.3010 | 83.0334 | 20012 | 500 | 19833 | 1424 | 93 | 6.5309 | |
| gduggal-bwaplat | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 84.3152 | 73.5419 | 98.7866 | 76.1775 | 1387 | 499 | 1384 | 17 | 13 | 76.4706 | |
| eyeh-varpipe | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 61.2415 | 62.4812 | 60.0500 | 60.0866 | 831 | 499 | 720 | 479 | 472 | 98.5386 | |
| eyeh-varpipe | INDEL | I1_5 | HG002complexvar | het | 97.2764 | 97.2566 | 97.2962 | 48.7706 | 17690 | 499 | 17129 | 476 | 444 | 93.2773 | |
| ltrigg-rtg2 | SNP | ti | map_l125_m2_e0 | het | 98.5679 | 97.3564 | 99.8099 | 58.2477 | 18377 | 499 | 18379 | 35 | 4 | 11.4286 | |
| anovak-vg | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 22.1529 | 0.0000 | 0.0000 | 142 | 499 | 0 | 0 | 0 | ||
| astatham-gatk | INDEL | D6_15 | * | * | 98.2985 | 98.0875 | 98.5103 | 54.9898 | 25593 | 499 | 25592 | 387 | 347 | 89.6641 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 0.0000 | 55.8407 | 0.0000 | 0.0000 | 631 | 499 | 0 | 0 | 0 | ||
| ghariani-varprowl | SNP | * | map_l100_m0_e0 | * | 97.6658 | 98.4806 | 96.8644 | 74.2691 | 32342 | 499 | 32344 | 1047 | 227 | 21.6810 | |
| hfeng-pmm1 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.9701 | 86.9508 | 99.8848 | 40.2923 | 3325 | 499 | 3468 | 4 | 4 | 100.0000 | |
| gduggal-snapplat | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 30.4336 | 32.6586 | 28.4924 | 77.1672 | 242 | 499 | 412 | 1034 | 214 | 20.6963 | |
| hfeng-pmm1 | INDEL | D1_5 | HG002complexvar | * | 99.1888 | 98.4747 | 99.9133 | 56.8376 | 32216 | 499 | 32267 | 28 | 18 | 64.2857 | |
| hfeng-pmm3 | INDEL | D6_15 | HG002compoundhet | hetalt | 96.8362 | 93.8781 | 99.9869 | 24.0528 | 7652 | 499 | 7656 | 1 | 0 | 0.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.5493 | 93.8357 | 99.4245 | 23.8294 | 7596 | 499 | 7602 | 44 | 43 | 97.7273 | |
| raldana-dualsentieon | SNP | tv | HG002compoundhet | het | 94.2957 | 89.3216 | 99.8564 | 53.2191 | 4174 | 499 | 4172 | 6 | 3 | 50.0000 | |
| jli-custom | SNP | * | map_l100_m2_e1 | * | 99.4761 | 99.3323 | 99.6202 | 63.1271 | 74238 | 499 | 74235 | 283 | 79 | 27.9152 | |
| ltrigg-rtg1 | SNP | * | map_l125_m0_e0 | * | 98.5751 | 97.4258 | 99.7517 | 64.2305 | 18886 | 499 | 18884 | 47 | 16 | 34.0426 | |
| jli-custom | SNP | * | map_l100_m2_e0 | * | 99.4726 | 99.3267 | 99.6190 | 63.1033 | 73466 | 498 | 73463 | 281 | 79 | 28.1139 | |
| ciseli-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 52.4859 | 43.1507 | 66.9753 | 66.7692 | 378 | 498 | 434 | 214 | 200 | 93.4579 | |
| gduggal-bwavard | INDEL | I6_15 | * | het | 71.5920 | 95.0364 | 57.4257 | 53.1216 | 9535 | 498 | 9512 | 7052 | 6790 | 96.2847 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 64.9523 | 50.2994 | 91.6515 | 76.9456 | 504 | 498 | 505 | 46 | 8 | 17.3913 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 93.0591 | 87.6396 | 99.1931 | 21.1150 | 3531 | 498 | 3565 | 29 | 24 | 82.7586 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 43.3030 | 29.1607 | 84.0796 | 50.0000 | 205 | 498 | 169 | 32 | 7 | 21.8750 | |
| gduggal-snapfb | INDEL | I1_5 | HG002complexvar | homalt | 96.0286 | 96.2968 | 95.7618 | 50.6870 | 12950 | 498 | 12992 | 575 | 251 | 43.6522 | |
| hfeng-pmm3 | SNP | tv | HG002compoundhet | * | 97.0510 | 94.4189 | 99.8341 | 47.0669 | 8425 | 498 | 8423 | 14 | 7 | 50.0000 | |
| hfeng-pmm2 | INDEL | D1_5 | HG002complexvar | * | 99.1842 | 98.4778 | 99.9009 | 57.1533 | 32217 | 498 | 32268 | 32 | 21 | 65.6250 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.8141 | 93.8481 | 99.9738 | 26.3153 | 7597 | 498 | 7631 | 2 | 1 | 50.0000 | |
| ltrigg-rtg2 | SNP | ti | map_l125_m1_e0 | het | 98.5415 | 97.2791 | 99.8371 | 55.5647 | 17769 | 497 | 17770 | 29 | 4 | 13.7931 | |
| astatham-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2511 | 98.5968 | 99.9141 | 62.3697 | 34922 | 497 | 34912 | 30 | 13 | 43.3333 | |
| bgallagher-sentieon | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.8385 | 87.0031 | 99.5129 | 39.9105 | 3327 | 497 | 3473 | 17 | 16 | 94.1176 | |
| gduggal-snapfb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 0.0000 | 0.0000 | 0.0000 | 0 | 497 | 0 | 0 | 0 | |||
| gduggal-snapplat | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 0.0000 | 0.0000 | 0.0000 | 0 | 497 | 0 | 0 | 0 | |||
| gduggal-snapvard | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 0.0000 | 0.0000 | 28.1250 | 61.4458 | 0 | 497 | 27 | 69 | 24 | 34.7826 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.1995 | 96.8094 | 99.6302 | 71.4676 | 15080 | 497 | 15087 | 56 | 47 | 83.9286 | |
| ckim-isaac | INDEL | D1_5 | map_l100_m1_e0 | * | 83.8870 | 73.1061 | 98.3977 | 82.4582 | 1351 | 497 | 1351 | 22 | 10 | 45.4545 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 82.5839 | 81.3183 | 83.8895 | 82.0997 | 2159 | 496 | 2187 | 420 | 360 | 85.7143 | |
| jli-custom | SNP | * | map_l100_m1_e0 | * | 99.4716 | 99.3149 | 99.6287 | 61.0483 | 71907 | 496 | 71904 | 268 | 79 | 29.4776 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 68.7772 | 52.7619 | 98.7522 | 77.3150 | 554 | 496 | 554 | 7 | 2 | 28.5714 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 38.1546 | 23.5747 | 100.0000 | 63.5697 | 153 | 496 | 149 | 0 | 0 | ||
| ckim-dragen | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 92.8661 | 87.0293 | 99.5422 | 40.0515 | 3328 | 496 | 3479 | 16 | 16 | 100.0000 | |
| bgallagher-sentieon | SNP | ti | * | het | 99.9232 | 99.9613 | 99.8851 | 18.4052 | 1281395 | 496 | 1281341 | 1474 | 76 | 5.1560 | |
| astatham-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.5419 | 95.5335 | 99.6365 | 30.2678 | 10609 | 496 | 10690 | 39 | 38 | 97.4359 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 96.2548 | 97.7351 | 94.8187 | 76.1564 | 21403 | 496 | 21393 | 1169 | 1072 | 91.7023 | |
| gduggal-snapfb | SNP | tv | map_l100_m2_e0 | * | 97.5647 | 98.0226 | 97.1111 | 71.6649 | 24538 | 495 | 24539 | 730 | 232 | 31.7808 | |