PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
31751-31800 / 86044 show all | |||||||||||||||
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.2896 | 93.1726 | 99.6223 | 27.3304 | 7615 | 558 | 7650 | 29 | 28 | 96.5517 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.3190 | 93.1715 | 99.6865 | 67.9236 | 614 | 45 | 636 | 2 | 2 | 100.0000 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.3190 | 93.1715 | 99.6865 | 67.9236 | 614 | 45 | 636 | 2 | 2 | 100.0000 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.3185 | 93.1715 | 99.6855 | 68.3267 | 614 | 45 | 634 | 2 | 2 | 100.0000 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.3185 | 93.1715 | 99.6855 | 68.3267 | 614 | 45 | 634 | 2 | 2 | 100.0000 | |
| asubramanian-gatk | INDEL | D16_PLUS | * | hetalt | 95.6218 | 93.1712 | 98.2048 | 39.4536 | 1801 | 132 | 2024 | 37 | 31 | 83.7838 | |
| jpowers-varprowl | INDEL | * | map_l125_m1_e0 | homalt | 95.9887 | 93.1694 | 98.9840 | 82.2879 | 682 | 50 | 682 | 7 | 4 | 57.1429 | |
| ghariani-varprowl | INDEL | * | map_l125_m1_e0 | homalt | 95.5851 | 93.1694 | 98.1295 | 82.8225 | 682 | 50 | 682 | 13 | 4 | 30.7692 | |
| rpoplin-dv42 | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 88.9263 | 93.1683 | 85.0537 | 75.7901 | 3764 | 276 | 3642 | 640 | 581 | 90.7813 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.8458 | 93.1665 | 98.6838 | 27.9872 | 6626 | 486 | 6673 | 89 | 86 | 96.6292 | |
| hfeng-pmm2 | INDEL | I6_15 | HG002compoundhet | * | 95.0368 | 93.1632 | 96.9873 | 36.8937 | 8176 | 600 | 8177 | 254 | 252 | 99.2126 | |
| cchapple-custom | INDEL | D6_15 | map_l125_m1_e0 | * | 93.7322 | 93.1624 | 94.3089 | 88.0234 | 109 | 8 | 116 | 7 | 3 | 42.8571 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 79.0557 | 93.1620 | 68.6595 | 75.7645 | 5981 | 439 | 5926 | 2705 | 2382 | 88.0591 | |
| gduggal-bwavard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 79.0557 | 93.1620 | 68.6595 | 75.7645 | 5981 | 439 | 5926 | 2705 | 2382 | 88.0591 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.5238 | 93.1587 | 98.0122 | 81.7675 | 640 | 47 | 641 | 13 | 7 | 53.8462 | |
| hfeng-pmm1 | INDEL | * | map_l250_m1_e0 | het | 94.6524 | 93.1579 | 96.1957 | 95.0297 | 177 | 13 | 177 | 7 | 1 | 14.2857 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 95.8385 | 93.1558 | 98.6804 | 28.6536 | 6683 | 491 | 6730 | 90 | 87 | 96.6667 | |
| gduggal-snapplat | SNP | tv | map_l125_m2_e0 | het | 93.2998 | 93.1527 | 93.4473 | 85.9522 | 9727 | 715 | 9726 | 682 | 352 | 51.6129 | |
| ghariani-varprowl | INDEL | * | map_l125_m2_e1 | homalt | 95.5600 | 93.1525 | 98.0952 | 83.9590 | 721 | 53 | 721 | 14 | 5 | 35.7143 | |
| jpowers-varprowl | INDEL | * | map_l125_m2_e1 | homalt | 95.9415 | 93.1525 | 98.9026 | 83.4356 | 721 | 53 | 721 | 8 | 5 | 62.5000 | |
| jli-custom | INDEL | D6_15 | map_l100_m2_e1 | hetalt | 95.7746 | 93.1507 | 98.5507 | 73.5632 | 68 | 5 | 68 | 1 | 0 | 0.0000 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 93.7592 | 93.1507 | 94.3756 | 73.2357 | 1836 | 135 | 1829 | 109 | 67 | 61.4679 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 93.7592 | 93.1507 | 94.3756 | 73.2357 | 1836 | 135 | 1829 | 109 | 67 | 61.4679 | |
| gduggal-bwafb | INDEL | D6_15 | map_l150_m1_e0 | * | 95.1788 | 93.1507 | 97.2973 | 90.6210 | 68 | 5 | 72 | 2 | 1 | 50.0000 | |
| egarrison-hhga | INDEL | D6_15 | map_l150_m1_e0 | * | 94.5007 | 93.1507 | 95.8904 | 90.7828 | 68 | 5 | 70 | 3 | 3 | 100.0000 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 86.6794 | 93.1497 | 81.0496 | 83.5702 | 2502 | 184 | 2502 | 585 | 8 | 1.3675 | |
| ltrigg-rtg1 | INDEL | D6_15 | * | hetalt | 96.1547 | 93.1490 | 99.3609 | 40.3300 | 7614 | 560 | 7618 | 49 | 49 | 100.0000 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 84.3679 | 93.1480 | 77.1005 | 68.0245 | 3317 | 244 | 3377 | 1003 | 177 | 17.6471 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.1036 | 93.1474 | 99.2537 | 35.9088 | 1536 | 113 | 1729 | 13 | 13 | 100.0000 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 95.7841 | 93.1472 | 98.5746 | 46.7673 | 14680 | 1080 | 25103 | 363 | 284 | 78.2369 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 94.2145 | 93.1450 | 95.3088 | 77.7623 | 2473 | 182 | 2438 | 120 | 91 | 75.8333 | |
| ckim-isaac | SNP | ti | HG002complexvar | het | 96.4266 | 93.1447 | 99.9482 | 15.3403 | 293188 | 21578 | 293343 | 152 | 18 | 11.8421 | |
| asubramanian-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 95.0937 | 93.1429 | 97.1279 | 35.7383 | 326 | 24 | 372 | 11 | 10 | 90.9091 | |
| bgallagher-sentieon | INDEL | I1_5 | * | hetalt | 96.4303 | 93.1398 | 99.9619 | 60.7048 | 10427 | 768 | 10489 | 4 | 4 | 100.0000 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 83.0914 | 93.1398 | 75.0000 | 56.9061 | 353 | 26 | 351 | 117 | 113 | 96.5812 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.2821 | 93.1389 | 99.6448 | 63.2266 | 543 | 40 | 561 | 2 | 2 | 100.0000 | |
| gduggal-snapvard | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 80.1599 | 93.1385 | 70.3560 | 81.4743 | 2932 | 216 | 2905 | 1224 | 64 | 5.2288 | |
| anovak-vg | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | het | 89.0850 | 93.1385 | 85.3697 | 68.5884 | 2932 | 216 | 3256 | 558 | 215 | 38.5305 | |
| bgallagher-sentieon | INDEL | I1_5 | HG002compoundhet | hetalt | 96.4336 | 93.1377 | 99.9714 | 55.3771 | 10410 | 767 | 10470 | 3 | 3 | 100.0000 | |
| asubramanian-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 85.4071 | 93.1373 | 78.8618 | 92.1305 | 95 | 7 | 97 | 26 | 3 | 11.5385 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 94.5274 | 93.1373 | 95.9596 | 92.6230 | 95 | 7 | 95 | 4 | 3 | 75.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 94.0594 | 93.1373 | 95.0000 | 59.1837 | 95 | 7 | 95 | 5 | 5 | 100.0000 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 86.2677 | 93.1373 | 80.3419 | 74.6753 | 95 | 7 | 94 | 23 | 22 | 95.6522 | |
| hfeng-pmm3 | INDEL | I6_15 | * | hetalt | 96.4340 | 93.1353 | 99.9750 | 38.6184 | 7964 | 587 | 8004 | 2 | 2 | 100.0000 | |
| ckim-dragen | INDEL | I6_15 | HG002complexvar | hetalt | 96.4437 | 93.1316 | 100.0000 | 55.3409 | 1139 | 84 | 1179 | 0 | 0 | ||
| asubramanian-gatk | INDEL | I6_15 | HG002complexvar | hetalt | 96.0912 | 93.1316 | 99.2450 | 56.3849 | 1139 | 84 | 1183 | 9 | 7 | 77.7778 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 74.2485 | 93.1298 | 61.7328 | 60.2144 | 1586 | 117 | 3299 | 2045 | 1364 | 66.6993 | |
| ciseli-custom | SNP | ti | HG002compoundhet | homalt | 81.8243 | 93.1296 | 72.9667 | 35.5461 | 6886 | 508 | 6872 | 2546 | 564 | 22.1524 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.1709 | 93.1280 | 99.4195 | 32.5705 | 6681 | 493 | 6679 | 39 | 39 | 100.0000 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.8883 | 93.1278 | 98.8175 | 40.7349 | 15557 | 1148 | 16463 | 197 | 178 | 90.3553 | |