PrecisionFDA
Truth Challenge
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Explore HG002 comparison results
Use this interactive explorer to filter all results across submission entries and multiple dimensions.
| Entry | Type | Subtype | Subset | Genotype | F-score | Recall | Precision | Frac_NA | Truth TP | Truth FN | Query TP | Query FP | FP gt | % FP ma | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
1501-1550 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | D1_5 | * | * | 97.5429 | 96.3222 | 98.7949 | 47.4402 | 141348 | 5397 | 141168 | 1722 | 1190 | 69.1057 | |
| ckim-isaac | SNP | tv | map_l100_m2_e0 | het | 79.2946 | 65.8300 | 99.6834 | 69.5147 | 10386 | 5391 | 10389 | 33 | 8 | 24.2424 | |
| jmaeng-gatk | SNP | * | map_l125_m1_e0 | het | 88.1536 | 81.0158 | 96.6706 | 86.7253 | 23002 | 5390 | 22996 | 792 | 51 | 6.4394 | |
| ckim-vqsr | SNP | ti | map_l100_m0_e0 | homalt | 46.9836 | 30.7049 | 100.0000 | 82.8803 | 2387 | 5387 | 2387 | 0 | 0 | ||
| ckim-isaac | SNP | tv | map_l150_m1_e0 | * | 67.1487 | 50.6415 | 99.6215 | 77.0250 | 5526 | 5386 | 5527 | 21 | 7 | 33.3333 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 78.1296 | 65.4234 | 96.9610 | 81.1140 | 10191 | 5386 | 10178 | 319 | 94 | 29.4671 | |
| gduggal-snapvard | INDEL | * | HG002complexvar | homalt | 88.0378 | 80.0821 | 97.7484 | 41.5287 | 21643 | 5383 | 21880 | 504 | 456 | 90.4762 | |
| ckim-gatk | SNP | * | map_l125_m1_e0 | het | 88.2494 | 81.0510 | 96.8511 | 86.4318 | 23012 | 5380 | 23006 | 748 | 54 | 7.2193 | |
| ckim-isaac | SNP | ti | map_l125_m2_e1 | homalt | 69.3119 | 53.0546 | 99.9342 | 64.5595 | 6079 | 5379 | 6079 | 4 | 4 | 100.0000 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 75.9388 | 61.7232 | 98.6618 | 39.1505 | 8661 | 5371 | 8184 | 111 | 101 | 90.9910 | |
| ghariani-varprowl | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 73.9195 | 72.9786 | 74.8850 | 67.4004 | 14495 | 5367 | 14485 | 4858 | 4633 | 95.3685 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 50.8522 | 34.3937 | 97.5171 | 49.4033 | 2811 | 5362 | 3142 | 80 | 77 | 96.2500 | |
| ckim-isaac | SNP | tv | map_l100_m1_e0 | het | 78.9057 | 65.2916 | 99.6931 | 67.8118 | 10066 | 5351 | 10069 | 31 | 8 | 25.8065 | |
| asubramanian-gatk | SNP | tv | map_l150_m2_e1 | het | 42.7242 | 27.1911 | 99.6507 | 95.4527 | 1998 | 5350 | 1997 | 7 | 1 | 14.2857 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 32.7321 | 22.6516 | 58.9793 | 55.7780 | 1565 | 5344 | 1537 | 1069 | 1020 | 95.4163 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 70.9466 | 66.7041 | 75.7654 | 53.5142 | 10704 | 5343 | 10864 | 3475 | 3422 | 98.4748 | |
| asubramanian-gatk | SNP | tv | HG002complexvar | het | 98.1875 | 96.4619 | 99.9759 | 22.1458 | 145398 | 5333 | 145329 | 35 | 10 | 28.5714 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 49.2492 | 43.6456 | 56.5037 | 39.7780 | 4128 | 5330 | 4231 | 3257 | 2430 | 74.6085 | |
| ckim-isaac | SNP | ti | map_l125_m2_e0 | homalt | 69.3312 | 53.0727 | 99.9503 | 64.5277 | 6028 | 5330 | 6028 | 3 | 3 | 100.0000 | |
| jpowers-varprowl | SNP | * | HG002complexvar | * | 99.4683 | 99.2937 | 99.6435 | 20.7160 | 749051 | 5328 | 749404 | 2681 | 1602 | 59.7538 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 50.6627 | 34.2063 | 97.6335 | 41.8233 | 2769 | 5326 | 3053 | 74 | 71 | 95.9459 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 75.6523 | 61.3266 | 98.7108 | 36.0827 | 8441 | 5323 | 7963 | 104 | 95 | 91.3462 | |
| mlin-fermikit | SNP | * | map_l250_m2_e1 | * | 47.5699 | 33.4544 | 82.2913 | 80.2109 | 2672 | 5315 | 2672 | 575 | 501 | 87.1304 | |
| qzeng-custom | SNP | ti | * | homalt | 99.6207 | 99.3383 | 99.9047 | 15.9860 | 797725 | 5314 | 792891 | 756 | 473 | 62.5661 | |
| gduggal-snapplat | INDEL | D6_15 | * | hetalt | 51.3567 | 35.1358 | 95.3989 | 60.4943 | 2872 | 5302 | 2882 | 139 | 111 | 79.8561 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 40.0585 | 36.9961 | 43.6736 | 81.3091 | 3111 | 5298 | 3179 | 4100 | 363 | 8.8537 | |
| asubramanian-gatk | SNP | tv | map_l150_m2_e0 | het | 42.5209 | 27.0270 | 99.6439 | 95.4728 | 1960 | 5292 | 1959 | 7 | 1 | 14.2857 | |
| ckim-isaac | INDEL | * | * | hetalt | 87.6357 | 79.0308 | 98.3434 | 43.3219 | 19945 | 5292 | 20303 | 342 | 304 | 88.8889 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 81.4087 | 70.0526 | 97.1590 | 70.4588 | 12379 | 5292 | 12380 | 362 | 254 | 70.1657 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 81.4087 | 70.0526 | 97.1590 | 70.4588 | 12379 | 5292 | 12380 | 362 | 254 | 70.1657 | |
| gduggal-snapfb | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 54.4986 | 47.4734 | 63.9642 | 60.7084 | 4782 | 5291 | 5499 | 3098 | 1349 | 43.5442 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 25.0146 | 16.3556 | 53.1570 | 69.3516 | 1034 | 5288 | 985 | 868 | 794 | 91.4747 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 25.0146 | 16.3556 | 53.1570 | 69.3516 | 1034 | 5288 | 985 | 868 | 794 | 91.4747 | |
| gduggal-snapplat | INDEL | D6_15 | HG002compoundhet | hetalt | 51.7417 | 35.1859 | 97.7226 | 44.3646 | 2868 | 5283 | 2875 | 67 | 52 | 77.6119 | |
| ckim-isaac | INDEL | * | HG002compoundhet | hetalt | 88.0188 | 79.0747 | 99.2444 | 32.7152 | 19911 | 5269 | 20095 | 153 | 126 | 82.3529 | |
| mlin-fermikit | SNP | * | map_l250_m2_e0 | * | 47.3085 | 33.2150 | 82.1776 | 79.9585 | 2619 | 5266 | 2619 | 568 | 495 | 87.1479 | |
| ckim-isaac | SNP | ti | map_l125_m1_e0 | homalt | 68.7652 | 52.4129 | 99.9482 | 60.3233 | 5789 | 5256 | 5789 | 3 | 3 | 100.0000 | |
| ckim-vqsr | SNP | ti | HG002complexvar | het | 99.1493 | 98.3302 | 99.9822 | 17.7224 | 309510 | 5256 | 309462 | 55 | 18 | 32.7273 | |
| asubramanian-gatk | SNP | tv | map_l125_m0_e0 | * | 34.3571 | 20.7510 | 99.7825 | 95.7011 | 1376 | 5255 | 1376 | 3 | 1 | 33.3333 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 76.5549 | 62.5570 | 98.6231 | 39.2209 | 8778 | 5254 | 8094 | 113 | 98 | 86.7257 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 51.1480 | 34.9051 | 95.6654 | 53.7872 | 2813 | 5246 | 2825 | 128 | 108 | 84.3750 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 51.1480 | 34.9051 | 95.6654 | 53.7872 | 2813 | 5246 | 2825 | 128 | 108 | 84.3750 | |
| gduggal-snapvard | SNP | * | map_siren | * | 96.2272 | 96.4179 | 96.0373 | 65.1379 | 140990 | 5238 | 139038 | 5737 | 591 | 10.3016 | |
| ghariani-varprowl | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 34.4349 | 24.2003 | 59.6699 | 64.4061 | 1672 | 5237 | 1663 | 1124 | 1036 | 92.1708 | |
| ciseli-custom | SNP | ti | map_l125_m2_e1 | het | 77.9434 | 72.5730 | 84.1721 | 81.0539 | 13852 | 5235 | 13848 | 2604 | 72 | 2.7650 | |
| ciseli-custom | SNP | * | map_l125_m0_e0 | * | 77.7410 | 73.0049 | 83.1343 | 80.5630 | 14152 | 5233 | 14132 | 2867 | 775 | 27.0317 | |
| ckim-vqsr | SNP | * | map_l125_m0_e0 | homalt | 36.1328 | 22.0501 | 100.0000 | 90.6459 | 1480 | 5232 | 1480 | 0 | 0 | ||
| ckim-isaac | INDEL | I6_15 | * | * | 86.2978 | 78.9268 | 95.1875 | 41.9911 | 19592 | 5231 | 19601 | 991 | 727 | 73.3602 | |
| qzeng-custom | SNP | ti | HG002complexvar | het | 99.0720 | 98.3388 | 99.8162 | 18.0479 | 309537 | 5229 | 307433 | 566 | 153 | 27.0318 | |
| mlin-fermikit | SNP | ti | map_l150_m0_e0 | * | 48.0167 | 33.6471 | 83.8086 | 63.2254 | 2645 | 5216 | 2645 | 511 | 462 | 90.4110 | |