PrecisionFDA
Truth Challenge
Engage and improve DNA test results with our community challenges
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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
25251-25300 / 86044 show all | |||||||||||||||
| ciseli-custom | SNP | * | HG002complexvar | * | 95.9712 | 96.9985 | 94.9655 | 20.7202 | 731742 | 22643 | 718679 | 38100 | 8358 | 21.9370 | |
| jmaeng-gatk | INDEL | I1_5 | map_l100_m0_e0 | het | 95.9708 | 98.1595 | 93.8776 | 91.6586 | 320 | 6 | 322 | 21 | 0 | 0.0000 | |
| jmaeng-gatk | INDEL | D6_15 | map_l100_m2_e1 | het | 95.9707 | 97.0370 | 94.9275 | 92.4672 | 131 | 4 | 131 | 7 | 2 | 28.5714 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 95.9707 | 98.1273 | 93.9068 | 59.2105 | 262 | 5 | 262 | 17 | 17 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | map_l100_m2_e1 | * | 95.9707 | 95.2727 | 96.6790 | 89.6919 | 262 | 13 | 262 | 9 | 2 | 22.2222 | |
| dgrover-gatk | INDEL | D6_15 | map_l100_m2_e1 | het | 95.9707 | 97.0370 | 94.9275 | 90.5802 | 131 | 4 | 131 | 7 | 2 | 28.5714 | |
| eyeh-varpipe | SNP | tv | map_l100_m1_e0 | het | 95.9704 | 99.7405 | 92.4749 | 70.7958 | 15377 | 40 | 15189 | 1236 | 16 | 1.2945 | |
| ckim-gatk | INDEL | I6_15 | * | hetalt | 95.9700 | 92.3167 | 99.9244 | 35.7056 | 7894 | 657 | 7935 | 6 | 5 | 83.3333 | |
| cchapple-custom | INDEL | * | map_l100_m2_e1 | * | 95.9700 | 96.4324 | 95.5120 | 84.7746 | 3622 | 134 | 3703 | 174 | 52 | 29.8851 | |
| jmaeng-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 95.9688 | 92.2844 | 99.9596 | 33.6636 | 2440 | 204 | 2476 | 1 | 1 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | map_l100_m0_e0 | het | 95.9671 | 94.7853 | 97.1787 | 91.9444 | 309 | 17 | 310 | 9 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | D1_5 | HG002compoundhet | * | 95.9661 | 94.4994 | 97.4791 | 66.2791 | 11562 | 673 | 11562 | 299 | 296 | 98.9967 | |
| dgrover-gatk | INDEL | I1_5 | map_l250_m2_e0 | * | 95.9641 | 94.6903 | 97.2727 | 96.6616 | 107 | 6 | 107 | 3 | 2 | 66.6667 | |
| ltrigg-rtg2 | INDEL | I6_15 | map_l100_m2_e0 | * | 95.9641 | 92.2414 | 100.0000 | 81.9298 | 107 | 9 | 103 | 0 | 0 | ||
| ltrigg-rtg2 | INDEL | I6_15 | map_l100_m2_e1 | * | 95.9641 | 92.2414 | 100.0000 | 82.3328 | 107 | 9 | 103 | 0 | 0 | ||
| astatham-gatk | INDEL | I6_15 | map_l100_m1_e0 | * | 95.9641 | 93.8596 | 98.1651 | 87.8348 | 107 | 7 | 107 | 2 | 1 | 50.0000 | |
| gduggal-bwafb | INDEL | * | tech_badpromoters | * | 95.9637 | 93.4211 | 98.6486 | 48.6111 | 71 | 5 | 73 | 1 | 1 | 100.0000 | |
| eyeh-varpipe | INDEL | I1_5 | HG002complexvar | * | 95.9629 | 94.9405 | 97.0075 | 49.9241 | 31675 | 1688 | 31023 | 957 | 917 | 95.8203 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 95.9629 | 98.6871 | 93.3851 | 38.4673 | 2255 | 30 | 2287 | 162 | 154 | 95.0617 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 95.9626 | 93.3863 | 98.6851 | 30.5076 | 7526 | 533 | 7580 | 101 | 97 | 96.0396 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 95.9626 | 93.3863 | 98.6851 | 30.5076 | 7526 | 533 | 7580 | 101 | 97 | 96.0396 | |
| cchapple-custom | SNP | ti | map_l250_m0_e0 | * | 95.9625 | 94.5985 | 97.3664 | 93.5930 | 1296 | 74 | 1294 | 35 | 13 | 37.1429 | |
| egarrison-hhga | INDEL | * | map_l250_m2_e1 | het | 95.9620 | 95.7346 | 96.1905 | 96.0667 | 202 | 9 | 202 | 8 | 2 | 25.0000 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 95.9616 | 93.1237 | 98.9779 | 28.5807 | 7611 | 562 | 7650 | 79 | 73 | 92.4051 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 95.9615 | 94.5946 | 97.3684 | 70.7692 | 35 | 2 | 37 | 1 | 1 | 100.0000 | |
| bgallagher-sentieon | INDEL | * | map_l250_m1_e0 | * | 95.9612 | 97.3770 | 94.5860 | 95.9242 | 297 | 8 | 297 | 17 | 4 | 23.5294 | |
| cchapple-custom | INDEL | * | map_l100_m1_e0 | * | 95.9601 | 96.4584 | 95.4668 | 83.7178 | 3459 | 127 | 3538 | 168 | 48 | 28.5714 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 95.9599 | 92.4574 | 99.7382 | 69.8024 | 380 | 31 | 381 | 1 | 1 | 100.0000 | |
| ckim-dragen | INDEL | * | * | hetalt | 95.9597 | 92.4793 | 99.7124 | 57.0557 | 23339 | 1898 | 23575 | 68 | 68 | 100.0000 | |
| ghariani-varprowl | SNP | tv | segdup | het | 95.9597 | 99.4326 | 92.7212 | 94.3028 | 5257 | 30 | 5261 | 413 | 3 | 0.7264 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.9595 | 93.9583 | 98.0477 | 81.2678 | 451 | 29 | 452 | 9 | 7 | 77.7778 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 95.9592 | 95.9184 | 96.0000 | 82.4561 | 47 | 2 | 48 | 2 | 2 | 100.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 95.9582 | 94.9341 | 97.0045 | 63.7624 | 3673 | 196 | 3627 | 112 | 107 | 95.5357 | |
| gduggal-snapfb | INDEL | I1_5 | map_l100_m2_e1 | * | 95.9578 | 96.3441 | 95.5746 | 86.0998 | 1344 | 51 | 1339 | 62 | 13 | 20.9677 | |
| gduggal-bwaplat | SNP | ti | HG002compoundhet | hetalt | 95.9569 | 92.2280 | 100.0000 | 21.9941 | 534 | 45 | 532 | 0 | 0 | ||
| gduggal-bwafb | INDEL | I1_5 | map_l125_m0_e0 | het | 95.9569 | 92.7083 | 99.4413 | 88.6493 | 178 | 14 | 178 | 1 | 0 | 0.0000 | |
| gduggal-snapvard | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 95.9560 | 96.0290 | 95.8832 | 44.2273 | 3313 | 137 | 3284 | 141 | 11 | 7.8014 | |
| jmaeng-gatk | INDEL | D6_15 | map_l100_m2_e1 | * | 95.9559 | 94.9091 | 97.0260 | 89.6974 | 261 | 14 | 261 | 8 | 3 | 37.5000 | |
| cchapple-custom | INDEL | C6_15 | * | * | 95.9554 | 100.0000 | 92.2252 | 93.7957 | 7 | 0 | 344 | 29 | 11 | 37.9310 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.9552 | 95.8879 | 96.0225 | 64.6127 | 3078 | 132 | 3066 | 127 | 123 | 96.8504 | |
| jli-custom | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 95.9552 | 93.5145 | 98.5267 | 75.6611 | 1067 | 74 | 1070 | 16 | 10 | 62.5000 | |
| ckim-isaac | SNP | * | HG002complexvar | * | 95.9550 | 92.3552 | 99.8467 | 16.9098 | 696714 | 57671 | 697067 | 1070 | 847 | 79.1589 | |
| ckim-vqsr | INDEL | I6_15 | HG002compoundhet | hetalt | 95.9547 | 92.2455 | 99.9747 | 28.2465 | 7875 | 662 | 7916 | 2 | 2 | 100.0000 | |
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 95.9540 | 95.2267 | 96.6924 | 48.5132 | 13127 | 658 | 13126 | 449 | 442 | 98.4410 | |
| hfeng-pmm1 | INDEL | D6_15 | HG002complexvar | het | 95.9519 | 92.8205 | 99.3019 | 57.0271 | 2896 | 224 | 2845 | 20 | 17 | 85.0000 | |
| ckim-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | * | 95.9513 | 95.9677 | 95.9350 | 99.9185 | 119 | 5 | 118 | 5 | 0 | 0.0000 | |
| cchapple-custom | SNP | * | map_l100_m0_e0 | het | 95.9513 | 97.0667 | 94.8612 | 75.7604 | 20583 | 622 | 20601 | 1116 | 255 | 22.8495 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 95.9473 | 92.9048 | 99.1959 | 36.3902 | 1532 | 117 | 1727 | 14 | 14 | 100.0000 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 95.9472 | 94.6281 | 97.3036 | 80.6048 | 916 | 52 | 830 | 23 | 15 | 65.2174 | |
| ndellapenna-hhga | INDEL | I1_5 | HG002compoundhet | * | 95.9469 | 94.5452 | 97.3908 | 62.1995 | 11682 | 674 | 11683 | 313 | 258 | 82.4281 | |