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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
17651-17700 / 86044 show all | |||||||||||||||
| anovak-vg | INDEL | D6_15 | map_l125_m2_e0 | het | 77.7080 | 80.2817 | 75.2941 | 89.6341 | 57 | 14 | 64 | 21 | 11 | 52.3810 | |
| anovak-vg | INDEL | D6_15 | map_l125_m2_e1 | het | 78.0093 | 80.2817 | 75.8621 | 89.5558 | 57 | 14 | 66 | 21 | 11 | 52.3810 | |
| anovak-vg | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_51to200 | * | 12.7389 | 8.0000 | 31.2500 | 63.6364 | 2 | 23 | 5 | 11 | 11 | 100.0000 | |
| anovak-vg | INDEL | I6_15 | map_siren | het | 45.1108 | 34.9650 | 63.5514 | 79.0607 | 50 | 93 | 68 | 39 | 11 | 28.2051 | |
| anovak-vg | SNP | tv | func_cds | homalt | 98.9685 | 98.7676 | 99.1701 | 25.0222 | 1683 | 21 | 1673 | 14 | 11 | 78.5714 | |
| anovak-vg | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 97.9774 | 97.8472 | 98.1079 | 69.1926 | 1409 | 31 | 1400 | 27 | 11 | 40.7407 | |
| astatham-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9292 | 99.9646 | 99.8938 | 56.3468 | 11292 | 4 | 11292 | 12 | 11 | 91.6667 | |
| astatham-gatk | INDEL | * | map_l100_m1_e0 | het | 95.1305 | 93.0201 | 97.3389 | 86.8492 | 2079 | 156 | 2085 | 57 | 11 | 19.2982 | |
| astatham-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.0766 | 96.6507 | 99.5451 | 88.1460 | 2626 | 91 | 2626 | 12 | 11 | 91.6667 | |
| astatham-gatk | SNP | * | map_l125_m0_e0 | homalt | 99.0469 | 98.3164 | 99.7883 | 67.5212 | 6599 | 113 | 6599 | 14 | 11 | 78.5714 | |
| astatham-gatk | SNP | ti | HG002compoundhet | het | 98.7553 | 97.6644 | 99.8709 | 39.9910 | 9283 | 222 | 9281 | 12 | 11 | 91.6667 | |
| astatham-gatk | SNP | tv | HG002complexvar | het | 98.5778 | 97.2116 | 99.9829 | 21.9634 | 146528 | 4203 | 146456 | 25 | 11 | 44.0000 | |
| astatham-gatk | SNP | tv | HG002compoundhet | het | 98.5818 | 97.4321 | 99.7590 | 55.5988 | 4553 | 120 | 4553 | 11 | 11 | 100.0000 | |
| astatham-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2005 | 98.5314 | 99.8788 | 66.3539 | 17310 | 258 | 17301 | 21 | 11 | 52.3810 | |
| astatham-gatk | SNP | tv | map_l100_m0_e0 | * | 93.1039 | 87.3962 | 99.6092 | 73.8497 | 9687 | 1397 | 9686 | 38 | 11 | 28.9474 | |
| astatham-gatk | SNP | tv | map_siren | het | 88.3820 | 79.2932 | 99.8239 | 66.9200 | 22685 | 5924 | 22680 | 40 | 11 | 27.5000 | |
| asubramanian-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.9354 | 98.2913 | 99.5879 | 51.8136 | 3624 | 63 | 3625 | 15 | 11 | 73.3333 | |
| asubramanian-gatk | INDEL | I16_PLUS | * | het | 96.3656 | 93.7454 | 99.1366 | 77.2113 | 2548 | 170 | 2526 | 22 | 11 | 50.0000 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 93.3398 | 93.6585 | 93.0233 | 91.4274 | 192 | 13 | 200 | 15 | 11 | 73.3333 | |
| asubramanian-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 93.3398 | 93.6585 | 93.0233 | 91.4274 | 192 | 13 | 200 | 15 | 11 | 73.3333 | |
| asubramanian-gatk | INDEL | I1_5 | HG002complexvar | hetalt | 97.2967 | 95.4229 | 99.2455 | 71.3930 | 1647 | 79 | 1710 | 13 | 11 | 84.6154 | |
| asubramanian-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.9820 | 98.8732 | 99.0909 | 66.0303 | 1053 | 12 | 1199 | 11 | 11 | 100.0000 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.4987 | 91.5493 | 97.6445 | 76.0021 | 455 | 42 | 456 | 11 | 11 | 100.0000 | |
| bgallagher-sentieon | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.5306 | 93.3042 | 97.8659 | 82.3181 | 641 | 46 | 642 | 14 | 11 | 78.5714 | |
| bgallagher-sentieon | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | * | 97.9665 | 96.2317 | 99.7649 | 58.1536 | 5516 | 216 | 5517 | 13 | 11 | 84.6154 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 91.4729 | 100.0000 | 84.2857 | 76.0274 | 59 | 0 | 59 | 11 | 11 | 100.0000 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.6047 | 90.1119 | 97.3790 | 63.5026 | 483 | 53 | 483 | 13 | 11 | 84.6154 | |
| bgallagher-sentieon | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 96.2264 | 100.0000 | 92.7273 | 77.4590 | 153 | 0 | 153 | 12 | 11 | 91.6667 | |
| bgallagher-sentieon | SNP | * | HG002compoundhet | het | 99.7460 | 99.7320 | 99.7601 | 45.7386 | 14140 | 38 | 14138 | 34 | 11 | 32.3529 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 99.3771 | 99.4898 | 99.2647 | 88.8454 | 1755 | 9 | 1755 | 13 | 11 | 84.6154 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.4720 | 99.4510 | 99.4930 | 87.3253 | 2355 | 13 | 2355 | 12 | 11 | 91.6667 | |
| bgallagher-sentieon | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 99.4119 | 99.4624 | 99.3614 | 80.8398 | 6846 | 37 | 6846 | 44 | 11 | 25.0000 | |
| bgallagher-sentieon | SNP | * | map_l100_m0_e0 | homalt | 99.6507 | 99.4320 | 99.8703 | 60.0283 | 11554 | 66 | 11554 | 15 | 11 | 73.3333 | |
| bgallagher-sentieon | SNP | tv | HG002compoundhet | * | 99.7142 | 99.7422 | 99.6862 | 48.7920 | 8900 | 23 | 8895 | 28 | 11 | 39.2857 | |
| bgallagher-sentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.8517 | 99.4416 | 98.2688 | 76.2612 | 9082 | 51 | 9082 | 160 | 11 | 6.8750 | |
| bgallagher-sentieon | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.8517 | 99.4416 | 98.2688 | 76.2612 | 9082 | 51 | 9082 | 160 | 11 | 6.8750 | |
| cchapple-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.2253 | 98.2265 | 98.2240 | 66.6515 | 720 | 13 | 719 | 13 | 11 | 84.6154 | |
| astatham-gatk | INDEL | D16_PLUS | HG002complexvar | het | 98.2855 | 98.6450 | 97.9287 | 68.7747 | 1092 | 15 | 851 | 18 | 11 | 61.1111 | |
| astatham-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 95.0943 | 99.2126 | 91.3043 | 54.0000 | 126 | 1 | 126 | 12 | 11 | 91.6667 | |
| astatham-gatk | INDEL | D1_5 | HG002complexvar | homalt | 99.8868 | 99.8962 | 99.8774 | 60.2109 | 10587 | 11 | 10592 | 13 | 11 | 84.6154 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 94.3126 | 89.6450 | 99.4931 | 30.6266 | 2121 | 245 | 2159 | 11 | 11 | 100.0000 | |
| astatham-gatk | INDEL | I16_PLUS | * | het | 98.4446 | 98.1604 | 98.7304 | 75.7581 | 2668 | 50 | 2644 | 34 | 11 | 32.3529 | |
| astatham-gatk | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 96.2264 | 100.0000 | 92.7273 | 77.1468 | 153 | 0 | 153 | 12 | 11 | 91.6667 | |
| asubramanian-gatk | SNP | tv | HG002compoundhet | * | 98.0032 | 96.5370 | 99.5145 | 49.4980 | 8614 | 309 | 8609 | 42 | 11 | 26.1905 | |
| asubramanian-gatk | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.1727 | 98.8666 | 99.4807 | 69.4042 | 3053 | 35 | 3065 | 16 | 11 | 68.7500 | |
| bgallagher-sentieon | INDEL | * | map_l100_m1_e0 | het | 98.0470 | 98.6577 | 97.4438 | 85.8435 | 2205 | 30 | 2211 | 58 | 11 | 18.9655 | |
| bgallagher-sentieon | INDEL | * | map_l100_m2_e0 | het | 98.0419 | 98.6129 | 97.4776 | 86.6167 | 2275 | 32 | 2280 | 59 | 11 | 18.6441 | |
| bgallagher-sentieon | INDEL | * | map_l100_m2_e1 | het | 98.0718 | 98.6342 | 97.5158 | 86.6842 | 2311 | 32 | 2316 | 59 | 11 | 18.6441 | |
| bgallagher-sentieon | INDEL | * | segdup | * | 98.9462 | 99.1393 | 98.7539 | 94.5996 | 2534 | 22 | 2536 | 32 | 11 | 34.3750 | |
| bgallagher-sentieon | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.1285 | 99.7807 | 98.4848 | 70.2320 | 910 | 2 | 910 | 14 | 11 | 78.5714 | |