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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
55251-55300 / 86044 show all | |||||||||||||||
| mlin-fermikit | INDEL | D16_PLUS | map_l125_m2_e0 | homalt | 32.0000 | 100.0000 | 19.0476 | 94.5170 | 4 | 0 | 4 | 17 | 3 | 17.6471 | |
| mlin-fermikit | INDEL | D16_PLUS | map_l125_m2_e1 | homalt | 32.0000 | 100.0000 | 19.0476 | 94.6292 | 4 | 0 | 4 | 17 | 3 | 17.6471 | |
| 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 | |
| jli-custom | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 99.3377 | 99.4935 | 99.1825 | 82.1709 | 4125 | 21 | 4125 | 34 | 6 | 17.6471 | |
| bgallagher-sentieon | SNP | ti | map_l100_m0_e0 | * | 99.2132 | 99.3340 | 99.0926 | 69.0197 | 21626 | 145 | 21623 | 198 | 35 | 17.6768 | |
| ghariani-varprowl | SNP | tv | map_l150_m2_e1 | * | 97.0647 | 98.4698 | 95.6992 | 81.5758 | 11326 | 176 | 11326 | 509 | 90 | 17.6817 | |
| gduggal-bwaplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 88.2450 | 80.8166 | 97.1772 | 89.7454 | 8729 | 2072 | 8744 | 254 | 45 | 17.7165 | |
| qzeng-custom | INDEL | I16_PLUS | HG002complexvar | het | 88.3834 | 86.1654 | 90.7186 | 58.7909 | 573 | 92 | 606 | 62 | 11 | 17.7419 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.5155 | 98.1227 | 98.9115 | 70.9579 | 28173 | 539 | 28169 | 310 | 55 | 17.7419 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.5155 | 98.1227 | 98.9115 | 70.9579 | 28173 | 539 | 28169 | 310 | 55 | 17.7419 | |
| gduggal-snapfb | SNP | tv | HG002complexvar | homalt | 99.3543 | 99.6457 | 99.0647 | 24.8993 | 94774 | 337 | 94793 | 895 | 159 | 17.7654 | |
| gduggal-snapvard | INDEL | D1_5 | map_l250_m0_e0 | * | 74.2857 | 100.0000 | 59.0909 | 96.7105 | 46 | 0 | 65 | 45 | 8 | 17.7778 | |
| gduggal-snapvard | INDEL | D1_5 | map_l250_m0_e0 | het | 68.9655 | 100.0000 | 52.6316 | 96.7037 | 33 | 0 | 50 | 45 | 8 | 17.7778 | |
| hfeng-pmm2 | SNP | tv | HG002complexvar | het | 99.7540 | 99.5389 | 99.9700 | 20.7785 | 150036 | 695 | 149957 | 45 | 8 | 17.7778 | |
| ckim-isaac | SNP | * | map_l150_m1_e0 | het | 73.7957 | 58.6094 | 99.6041 | 78.9632 | 11321 | 7995 | 11322 | 45 | 8 | 17.7778 | |
| ckim-isaac | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | het | 92.2085 | 86.7552 | 98.3934 | 61.1512 | 2679 | 409 | 2756 | 45 | 8 | 17.7778 | |
| gduggal-bwaplat | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 91.1118 | 85.3688 | 97.6832 | 88.4817 | 5683 | 974 | 5692 | 135 | 24 | 17.7778 | |
| ckim-dragen | INDEL | * | map_l125_m0_e0 | * | 95.5436 | 96.1451 | 94.9495 | 90.2750 | 848 | 34 | 846 | 45 | 8 | 17.7778 | |
| bgallagher-sentieon | SNP | ti | map_l125_m2_e1 | * | 99.3333 | 99.4373 | 99.2295 | 72.6907 | 30397 | 172 | 30393 | 236 | 42 | 17.7966 | |
| gduggal-snapfb | INDEL | * | map_l100_m1_e0 | het | 93.1246 | 91.6331 | 94.6655 | 81.5482 | 2048 | 187 | 2094 | 118 | 21 | 17.7966 | |
| gduggal-bwafb | SNP | tv | map_l125_m1_e0 | het | 98.1591 | 98.7359 | 97.5891 | 74.7511 | 9998 | 128 | 9998 | 247 | 44 | 17.8138 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 49.9128 | 37.3964 | 75.0227 | 61.0403 | 902 | 1510 | 826 | 275 | 49 | 17.8182 | |
| ciseli-custom | SNP | ti | map_l250_m0_e0 | * | 69.6954 | 66.4234 | 73.3065 | 95.3499 | 910 | 460 | 909 | 331 | 59 | 17.8248 | |
| ckim-dragen | INDEL | D16_PLUS | map_l100_m2_e1 | * | 82.6291 | 90.7216 | 75.8621 | 95.5021 | 88 | 9 | 88 | 28 | 5 | 17.8571 | |
| ghariani-varprowl | SNP | tv | map_l150_m2_e0 | * | 97.0484 | 98.4500 | 95.6860 | 81.5364 | 11179 | 176 | 11179 | 504 | 90 | 17.8571 | |
| ghariani-varprowl | INDEL | * | map_l250_m1_e0 | het | 85.3147 | 96.3158 | 76.5690 | 97.3834 | 183 | 7 | 183 | 56 | 10 | 17.8571 | |
| ghariani-varprowl | INDEL | D1_5 | map_l150_m1_e0 | * | 90.5611 | 95.6764 | 85.9649 | 90.8486 | 686 | 31 | 686 | 112 | 20 | 17.8571 | |
| hfeng-pmm3 | INDEL | * | map_l100_m1_e0 | het | 98.5219 | 98.2998 | 98.7450 | 82.8675 | 2197 | 38 | 2203 | 28 | 5 | 17.8571 | |
| jlack-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.7667 | 98.9130 | 98.6207 | 68.3258 | 2002 | 22 | 2002 | 28 | 5 | 17.8571 | |
| hfeng-pmm1 | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1579 | 98.4076 | 99.9197 | 59.2367 | 34855 | 564 | 34845 | 28 | 5 | 17.8571 | |
| bgallagher-sentieon | SNP | * | map_l250_m2_e1 | het | 98.0666 | 98.7652 | 97.3778 | 90.6744 | 5199 | 65 | 5199 | 140 | 25 | 17.8571 | |
| ckim-isaac | SNP | ti | map_l150_m1_e0 | * | 71.6515 | 55.9050 | 99.7466 | 75.8793 | 11020 | 8692 | 11020 | 28 | 5 | 17.8571 | |
| dgrover-gatk | SNP | ti | map_l150_m0_e0 | het | 98.5705 | 98.7836 | 98.3584 | 84.6267 | 5035 | 62 | 5033 | 84 | 15 | 17.8571 | |
| dgrover-gatk | SNP | tv | map_l150_m2_e0 | het | 98.8320 | 99.2002 | 98.4666 | 81.2986 | 7194 | 58 | 7192 | 112 | 20 | 17.8571 | |
| dgrover-gatk | SNP | tv | map_l150_m2_e1 | het | 98.8473 | 99.2107 | 98.4865 | 81.3098 | 7290 | 58 | 7288 | 112 | 20 | 17.8571 | |
| bgallagher-sentieon | SNP | ti | map_l125_m2_e0 | * | 99.3281 | 99.4316 | 99.2249 | 72.6504 | 30086 | 172 | 30082 | 235 | 42 | 17.8723 | |
| ghariani-varprowl | INDEL | D1_5 | map_l100_m0_e0 | het | 89.8148 | 98.4772 | 82.5532 | 89.6186 | 582 | 9 | 582 | 123 | 22 | 17.8862 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 88.8749 | 91.2134 | 86.6534 | 76.1180 | 436 | 42 | 435 | 67 | 12 | 17.9104 | |
| gduggal-snapfb | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 97.7559 | 98.8212 | 96.7133 | 52.5820 | 3940 | 47 | 3943 | 134 | 24 | 17.9104 | |
| bgallagher-sentieon | SNP | * | map_l250_m1_e0 | het | 97.9332 | 98.6540 | 97.2228 | 90.1965 | 4691 | 64 | 4691 | 134 | 24 | 17.9104 | |
| cchapple-custom | INDEL | * | map_l125_m2_e0 | het | 94.6558 | 96.3336 | 93.0355 | 88.2941 | 1340 | 51 | 1416 | 106 | 19 | 17.9245 | |
| cchapple-custom | INDEL | * | map_l125_m2_e1 | het | 94.7170 | 96.3778 | 93.1124 | 88.4024 | 1357 | 51 | 1433 | 106 | 19 | 17.9245 | |
| anovak-vg | INDEL | I16_PLUS | * | het | 20.3076 | 12.3988 | 56.0773 | 46.0104 | 337 | 2381 | 406 | 318 | 57 | 17.9245 | |
| ghariani-varprowl | INDEL | D1_5 | map_l150_m1_e0 | het | 89.3697 | 98.5477 | 81.7556 | 92.0269 | 475 | 7 | 475 | 106 | 19 | 17.9245 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 51.8064 | 59.5808 | 45.8266 | 64.9803 | 597 | 405 | 571 | 675 | 121 | 17.9259 | |
| gduggal-bwafb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 98.6534 | 99.7468 | 97.5836 | 59.0978 | 1576 | 4 | 1575 | 39 | 7 | 17.9487 | |
| mlin-fermikit | SNP | ti | HG002complexvar | het | 98.1941 | 96.4761 | 99.9743 | 15.7268 | 303674 | 11092 | 303641 | 78 | 14 | 17.9487 | |
| jlack-gatk | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.6565 | 98.6074 | 98.7056 | 69.5164 | 2974 | 42 | 2974 | 39 | 7 | 17.9487 | |
| hfeng-pmm2 | INDEL | * | map_l150_m2_e1 | * | 97.8966 | 98.4712 | 97.3288 | 90.4206 | 1417 | 22 | 1421 | 39 | 7 | 17.9487 | |
| qzeng-custom | INDEL | D16_PLUS | * | homalt | 83.8251 | 97.1040 | 73.7410 | 65.8948 | 1643 | 49 | 1640 | 584 | 105 | 17.9795 | |