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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
27351-27400 / 86044 show all | |||||||||||||||
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.9167 | 99.3224 | 98.5143 | 47.0103 | 2785 | 19 | 2785 | 42 | 42 | 100.0000 | |
| ltrigg-rtg1 | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 86.9857 | 77.8731 | 98.5138 | 67.0860 | 454 | 129 | 464 | 7 | 7 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.8289 | 99.1468 | 98.5131 | 59.7388 | 7321 | 63 | 7288 | 110 | 106 | 96.3636 | |
| gduggal-snapvard | INDEL | I1_5 | map_l150_m2_e1 | homalt | 94.7029 | 91.1765 | 98.5130 | 83.5474 | 186 | 18 | 265 | 4 | 2 | 50.0000 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 98.9118 | 99.3147 | 98.5122 | 62.5969 | 15652 | 108 | 15494 | 234 | 208 | 88.8889 | |
| jli-custom | SNP | tv | map_l250_m0_e0 | * | 96.8085 | 95.1634 | 98.5115 | 89.9973 | 728 | 37 | 728 | 11 | 5 | 45.4545 | |
| raldana-dualsentieon | SNP | tv | map_l250_m1_e0 | * | 98.0065 | 97.5066 | 98.5115 | 87.3534 | 2581 | 66 | 2581 | 39 | 3 | 7.6923 | |
| gduggal-bwaplat | INDEL | * | HG002complexvar | homalt | 93.8564 | 89.6215 | 98.5114 | 56.9159 | 24222 | 2805 | 24155 | 365 | 314 | 86.0274 | |
| ltrigg-rtg2 | INDEL | * | map_l100_m2_e1 | het | 97.4082 | 96.3295 | 98.5114 | 78.5661 | 2257 | 86 | 2250 | 34 | 4 | 11.7647 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m2_e1 | het | 98.7031 | 98.8959 | 98.5110 | 85.7047 | 1254 | 14 | 1257 | 19 | 3 | 15.7895 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 94.5857 | 90.9615 | 98.5106 | 44.8835 | 2838 | 282 | 2844 | 43 | 39 | 90.6977 | |
| jmaeng-gatk | SNP | ti | map_l100_m2_e1 | * | 90.0240 | 82.8837 | 98.5106 | 78.5961 | 41015 | 8470 | 41008 | 620 | 64 | 10.3226 | |
| gduggal-bwafb | INDEL | I1_5 | map_l125_m1_e0 | het | 96.4347 | 94.4444 | 98.5106 | 85.0794 | 459 | 27 | 463 | 7 | 1 | 14.2857 | |
| bgallagher-sentieon | INDEL | * | segdup | het | 98.8787 | 99.2497 | 98.5105 | 95.1038 | 1455 | 11 | 1455 | 22 | 2 | 9.0909 | |
| astatham-gatk | INDEL | D6_15 | * | * | 98.2985 | 98.0875 | 98.5103 | 54.9898 | 25593 | 499 | 25592 | 387 | 347 | 89.6641 | |
| ltrigg-rtg1 | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.1721 | 99.8428 | 98.5103 | 52.2176 | 2540 | 4 | 2579 | 39 | 0 | 0.0000 | |
| rpoplin-dv42 | SNP | ti | map_l250_m2_e1 | het | 98.3298 | 98.1510 | 98.5093 | 88.6573 | 3238 | 61 | 3238 | 49 | 29 | 59.1837 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 94.2933 | 90.4234 | 98.5092 | 63.1853 | 17704 | 1875 | 17841 | 270 | 18 | 6.6667 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 94.2933 | 90.4234 | 98.5092 | 63.1853 | 17704 | 1875 | 17841 | 270 | 18 | 6.6667 | |
| gduggal-bwafb | SNP | * | map_l125_m0_e0 | * | 98.4673 | 98.4266 | 98.5079 | 76.7395 | 19080 | 305 | 19080 | 289 | 76 | 26.2976 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 91.7362 | 85.8358 | 98.5078 | 31.2346 | 7975 | 1316 | 8252 | 125 | 116 | 92.8000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 91.7362 | 85.8358 | 98.5078 | 31.2346 | 7975 | 1316 | 8252 | 125 | 116 | 92.8000 | |
| ckim-isaac | SNP | * | tech_badpromoters | het | 91.6667 | 85.7143 | 98.5075 | 37.9630 | 66 | 11 | 66 | 1 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 74.7966 | 60.2857 | 98.5075 | 44.9315 | 211 | 139 | 198 | 3 | 2 | 66.6667 | |
| egarrison-hhga | INDEL | I1_5 | map_l150_m0_e0 | homalt | 98.5075 | 98.5075 | 98.5075 | 89.3142 | 66 | 1 | 66 | 1 | 1 | 100.0000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 81.7599 | 69.8795 | 98.5075 | 30.9278 | 58 | 25 | 66 | 1 | 1 | 100.0000 | |
| ckim-isaac | SNP | tv | tech_badpromoters | * | 94.9640 | 91.6667 | 98.5075 | 27.9570 | 66 | 6 | 66 | 1 | 0 | 0.0000 | |
| ghariani-varprowl | INDEL | I1_5 | map_l125_m2_e1 | homalt | 97.3451 | 96.2099 | 98.5075 | 80.6134 | 330 | 13 | 330 | 5 | 3 | 60.0000 | |
| cchapple-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.2481 | 100.0000 | 98.5075 | 67.1569 | 68 | 0 | 66 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | INDEL | D6_15 | map_l100_m2_e1 | homalt | 98.5075 | 98.5075 | 98.5075 | 84.8073 | 66 | 1 | 66 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | INDEL | D6_15 | map_l125_m2_e0 | het | 95.6522 | 92.9577 | 98.5075 | 89.2456 | 66 | 5 | 66 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | INDEL | D6_15 | map_l125_m2_e1 | het | 95.6522 | 92.9577 | 98.5075 | 89.4155 | 66 | 5 | 66 | 1 | 1 | 100.0000 | |
| raldana-dualsentieon | INDEL | I1_5 | map_l150_m0_e0 | homalt | 98.5075 | 98.5075 | 98.5075 | 87.2624 | 66 | 1 | 66 | 1 | 1 | 100.0000 | |
| ltrigg-rtg1 | INDEL | I1_5 | map_l150_m2_e0 | homalt | 99.2481 | 100.0000 | 98.5075 | 88.2181 | 201 | 0 | 198 | 3 | 1 | 33.3333 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 86.7676 | 77.5281 | 98.5075 | 65.9033 | 138 | 40 | 132 | 2 | 2 | 100.0000 | |
| jpowers-varprowl | INDEL | * | map_l125_m0_e0 | homalt | 95.6522 | 92.9577 | 98.5075 | 86.7063 | 264 | 20 | 264 | 4 | 3 | 75.0000 | |
| hfeng-pmm3 | INDEL | I1_5 | map_l150_m1_e0 | homalt | 99.2481 | 100.0000 | 98.5075 | 84.9099 | 198 | 0 | 198 | 3 | 2 | 66.6667 | |
| hfeng-pmm2 | INDEL | I1_5 | map_l150_m1_e0 | homalt | 99.2481 | 100.0000 | 98.5075 | 85.6017 | 198 | 0 | 198 | 3 | 2 | 66.6667 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 86.4432 | 77.0115 | 98.5075 | 99.9051 | 67 | 20 | 66 | 1 | 0 | 0.0000 | |
| hfeng-pmm1 | INDEL | I1_5 | map_l150_m1_e0 | homalt | 99.2481 | 100.0000 | 98.5075 | 85.7548 | 198 | 0 | 198 | 3 | 2 | 66.6667 | |
| jli-custom | INDEL | D1_5 | map_l100_m2_e1 | het | 98.6620 | 98.8170 | 98.5075 | 82.6685 | 1253 | 15 | 1254 | 19 | 5 | 26.3158 | |
| jli-custom | INDEL | I1_5 | map_l150_m1_e0 | homalt | 99.2481 | 100.0000 | 98.5075 | 85.5603 | 198 | 0 | 198 | 3 | 2 | 66.6667 | |
| astatham-gatk | INDEL | I1_5 | map_l150_m1_e0 | homalt | 99.2481 | 100.0000 | 98.5075 | 86.7676 | 198 | 0 | 198 | 3 | 2 | 66.6667 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.1659 | 95.8604 | 98.5075 | 61.5311 | 1181 | 51 | 1188 | 18 | 14 | 77.7778 | |
| bgallagher-sentieon | INDEL | I1_5 | map_l150_m1_e0 | homalt | 99.2481 | 100.0000 | 98.5075 | 86.5010 | 198 | 0 | 198 | 3 | 2 | 66.6667 | |
| mlin-fermikit | SNP | tv | map_l100_m2_e0 | het | 70.4610 | 54.8457 | 98.5073 | 60.6122 | 8653 | 7124 | 8645 | 131 | 2 | 1.5267 | |
| jmaeng-gatk | SNP | ti | map_l100_m2_e0 | * | 89.9408 | 82.7455 | 98.5068 | 78.6206 | 40513 | 8448 | 40506 | 614 | 64 | 10.4235 | |
| hfeng-pmm3 | INDEL | * | map_l125_m2_e1 | het | 98.2939 | 98.0824 | 98.5064 | 86.5724 | 1381 | 27 | 1385 | 21 | 3 | 14.2857 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.8761 | 99.2488 | 98.5061 | 62.8641 | 1057 | 8 | 1055 | 16 | 16 | 100.0000 | |
| rpoplin-dv42 | INDEL | * | map_l125_m2_e1 | * | 98.0600 | 97.6180 | 98.5061 | 98.7184 | 2172 | 53 | 2176 | 33 | 14 | 42.4242 | |