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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
54701-54750 / 86044 show all | |||||||||||||||
| bgallagher-sentieon | INDEL | I6_15 | HG002compoundhet | homalt | 14.4522 | 100.0000 | 7.7889 | 57.4332 | 31 | 0 | 31 | 367 | 366 | 99.7275 | |
| gduggal-snapplat | INDEL | I1_5 | HG002complexvar | homalt | 83.8960 | 77.5134 | 91.4241 | 57.4270 | 10424 | 3024 | 10586 | 993 | 140 | 14.0987 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 94.8184 | 97.5347 | 92.2494 | 57.4247 | 633 | 16 | 1095 | 92 | 89 | 96.7391 | |
| jpowers-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 46.9190 | 44.4652 | 49.6593 | 57.4245 | 19269 | 24066 | 19242 | 19506 | 19313 | 99.0106 | |
| gduggal-bwafb | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.2884 | 98.8435 | 99.7372 | 57.4242 | 16239 | 190 | 16321 | 43 | 29 | 67.4419 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 40.8888 | 58.1818 | 31.5202 | 57.4228 | 224 | 161 | 226 | 491 | 480 | 97.7597 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 90.6233 | 84.1577 | 98.1651 | 57.4219 | 1089 | 205 | 107 | 2 | 2 | 100.0000 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 85.0207 | 91.2790 | 79.5656 | 57.4207 | 16265 | 1554 | 15972 | 4102 | 4011 | 97.7816 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 58.6790 | 56.6022 | 60.9139 | 57.4205 | 12594 | 9656 | 12597 | 8083 | 5610 | 69.4049 | |
| ckim-isaac | SNP | tv | map_l100_m1_e0 | homalt | 68.8845 | 52.5489 | 99.9579 | 57.4205 | 4752 | 4291 | 4752 | 2 | 2 | 100.0000 | |
| gduggal-snapvard | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 55.6896 | 75.0355 | 44.2746 | 57.4199 | 1058 | 352 | 2664 | 3353 | 2340 | 69.7882 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 88.1349 | 97.1942 | 80.6205 | 57.4187 | 13371 | 386 | 13903 | 3342 | 3177 | 95.0628 | |
| ndellapenna-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 88.1349 | 97.1942 | 80.6205 | 57.4187 | 13371 | 386 | 13903 | 3342 | 3177 | 95.0628 | |
| mlin-fermikit | SNP | * | map_l125_m2_e1 | homalt | 66.2819 | 58.2991 | 76.7977 | 57.4167 | 10221 | 7311 | 10221 | 3088 | 2926 | 94.7539 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.0488 | 98.8712 | 99.2269 | 57.4163 | 6657 | 76 | 6931 | 54 | 10 | 18.5185 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.1492 | 98.5802 | 99.7249 | 57.4159 | 19580 | 282 | 19573 | 54 | 32 | 59.2593 | |
| dgrover-gatk | SNP | ti | map_l100_m1_e0 | homalt | 99.7294 | 99.5323 | 99.9273 | 57.4153 | 17876 | 84 | 17876 | 13 | 11 | 84.6154 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.7285 | 99.4585 | 100.0000 | 57.4142 | 3857 | 21 | 3857 | 0 | 0 | ||
| gduggal-bwafb | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 95.0569 | 99.3663 | 91.1057 | 57.4139 | 5645 | 36 | 5644 | 551 | 548 | 99.4555 | |
| hfeng-pmm2 | INDEL | I6_15 | HG002complexvar | * | 98.1553 | 97.1411 | 99.1910 | 57.4123 | 4655 | 137 | 4659 | 38 | 37 | 97.3684 | |
| astatham-gatk | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3009 | 98.6611 | 99.9489 | 57.4118 | 17612 | 239 | 17611 | 9 | 2 | 22.2222 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.3586 | 98.2333 | 98.4842 | 57.4113 | 6561 | 118 | 6562 | 101 | 80 | 79.2079 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 98.1705 | 99.5602 | 96.8190 | 57.4112 | 3622 | 16 | 3622 | 119 | 117 | 98.3193 | |
| qzeng-custom | INDEL | C16_PLUS | HG002compoundhet | homalt | 0.0000 | 0.0000 | 57.4074 | 0 | 0 | 0 | 23 | 0 | 0.0000 | ||
| ckim-isaac | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 97.8461 | 95.8323 | 99.9464 | 57.4072 | 3725 | 162 | 3727 | 2 | 2 | 100.0000 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 60.1668 | 61.4104 | 58.9725 | 57.4072 | 5164 | 3245 | 7289 | 5071 | 4386 | 86.4918 | |
| ckim-dragen | INDEL | * | HG002complexvar | homalt | 99.5434 | 99.8039 | 99.2843 | 57.4048 | 26974 | 53 | 26911 | 194 | 188 | 96.9072 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.3153 | 96.9789 | 99.6891 | 57.4040 | 1605 | 50 | 1603 | 5 | 2 | 40.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6954 | 99.5943 | 99.7967 | 57.4026 | 491 | 2 | 491 | 1 | 0 | 0.0000 | |
| ckim-dragen | SNP | ti | map_l100_m2_e0 | homalt | 99.6194 | 99.3610 | 99.8792 | 57.3994 | 18192 | 117 | 18197 | 22 | 20 | 90.9091 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 85.9526 | 84.9119 | 87.0190 | 57.3989 | 1784 | 317 | 1696 | 253 | 247 | 97.6285 | |
| hfeng-pmm3 | INDEL | * | * | hetalt | 96.7703 | 93.7869 | 99.9498 | 57.3944 | 23669 | 1568 | 23894 | 12 | 10 | 83.3333 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 47.2065 | 34.2838 | 75.7645 | 57.3941 | 1022 | 1959 | 991 | 317 | 53 | 16.7192 | |
| jpowers-varprowl | SNP | tv | HG002compoundhet | * | 83.9956 | 84.7697 | 83.2355 | 57.3909 | 7564 | 1359 | 7661 | 1543 | 1144 | 74.1413 | |
| asubramanian-gatk | INDEL | * | HG002complexvar | homalt | 99.4823 | 99.5116 | 99.4530 | 57.3903 | 26895 | 132 | 26910 | 148 | 101 | 68.2432 | |
| ckim-dragen | SNP | ti | map_l100_m2_e1 | homalt | 99.6178 | 99.3565 | 99.8804 | 57.3860 | 18375 | 119 | 18380 | 22 | 20 | 90.9091 | |
| jli-custom | INDEL | D16_PLUS | HG002compoundhet | het | 91.9260 | 95.5556 | 88.5621 | 57.3816 | 387 | 18 | 271 | 35 | 34 | 97.1429 | |
| raldana-dualsentieon | INDEL | D16_PLUS | HG002compoundhet | het | 81.9000 | 89.8765 | 75.2239 | 57.3791 | 364 | 41 | 252 | 83 | 82 | 98.7952 | |
| gduggal-snapvard | SNP | * | tech_badpromoters | het | 86.4516 | 87.0130 | 85.8974 | 57.3770 | 67 | 10 | 67 | 11 | 2 | 18.1818 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 73.2394 | 57.7778 | 100.0000 | 57.3770 | 26 | 19 | 26 | 0 | 0 | ||
| egarrison-hhga | INDEL | D6_15 | HG002complexvar | * | 89.5440 | 86.4579 | 92.8586 | 57.3769 | 4584 | 718 | 4590 | 353 | 276 | 78.1870 | |
| hfeng-pmm3 | INDEL | D16_PLUS | HG002compoundhet | het | 85.4445 | 90.8642 | 80.6349 | 57.3748 | 368 | 37 | 254 | 61 | 60 | 98.3607 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 75.2916 | 86.8093 | 66.4721 | 57.3739 | 6410 | 974 | 6834 | 3447 | 1755 | 50.9138 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.9545 | 96.0747 | 99.9093 | 57.3738 | 5507 | 225 | 5507 | 5 | 4 | 80.0000 | |
| ltrigg-rtg2 | SNP | tv | map_l125_m2_e1 | het | 98.4798 | 97.2993 | 99.6893 | 57.3735 | 10268 | 285 | 10267 | 32 | 2 | 6.2500 | |
| cchapple-custom | SNP | * | map_l100_m0_e0 | homalt | 98.1150 | 96.3081 | 99.9911 | 57.3704 | 11191 | 429 | 11188 | 1 | 1 | 100.0000 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | * | 80.2168 | 80.4348 | 80.0000 | 57.3643 | 37 | 9 | 44 | 11 | 6 | 54.5455 | |
| bgallagher-sentieon | INDEL | * | HG002complexvar | homalt | 99.7010 | 99.9186 | 99.4844 | 57.3638 | 27005 | 22 | 27015 | 140 | 135 | 96.4286 | |
| ltrigg-rtg1 | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.8395 | 99.7434 | 99.9357 | 57.3637 | 10883 | 28 | 10887 | 7 | 4 | 57.1429 | |
| asubramanian-gatk | INDEL | I1_5 | HG002complexvar | * | 99.2344 | 98.6572 | 99.8183 | 57.3625 | 32915 | 448 | 32967 | 60 | 50 | 83.3333 | |