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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
28301-28350 / 86044 show all | |||||||||||||||
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 97.3822 | 96.3731 | 98.4127 | 91.0490 | 372 | 14 | 372 | 6 | 4 | 66.6667 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 97.0803 | 96.3768 | 97.7941 | 91.0703 | 266 | 10 | 266 | 6 | 4 | 66.6667 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.6562 | 99.3685 | 99.9455 | 58.6114 | 11014 | 70 | 11010 | 6 | 4 | 66.6667 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.9371 | 98.3926 | 99.4876 | 28.3354 | 1163 | 19 | 1165 | 6 | 6 | 100.0000 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.4615 | 100.0000 | 96.9697 | 47.4801 | 192 | 0 | 192 | 6 | 5 | 83.3333 | |
| dgrover-gatk | INDEL | I16_PLUS | HG002complexvar | homalt | 99.0385 | 100.0000 | 98.0952 | 70.7521 | 309 | 0 | 309 | 6 | 6 | 100.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.6602 | 96.7890 | 98.5472 | 85.8707 | 422 | 14 | 407 | 6 | 4 | 66.6667 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 93.1818 | 100.0000 | 87.2340 | 88.3663 | 41 | 0 | 41 | 6 | 6 | 100.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | map_siren | * | 95.4928 | 97.6744 | 93.4066 | 92.6790 | 84 | 2 | 85 | 6 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | map_siren | het | 93.2039 | 97.9592 | 88.8889 | 91.7808 | 48 | 1 | 48 | 6 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l125_m0_e0 | * | 98.0676 | 98.0645 | 98.0707 | 89.6815 | 304 | 6 | 305 | 6 | 2 | 33.3333 | |
| dgrover-gatk | INDEL | I1_5 | map_l125_m1_e0 | het | 98.3497 | 97.9424 | 98.7603 | 87.9181 | 476 | 10 | 478 | 6 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l125_m2_e0 | het | 98.3863 | 97.9879 | 98.7879 | 88.9681 | 487 | 10 | 489 | 6 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l125_m2_e1 | het | 98.4213 | 98.0315 | 98.8142 | 89.0239 | 498 | 10 | 500 | 6 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_siren | homalt | 99.6298 | 99.7525 | 99.5074 | 78.6951 | 1209 | 3 | 1212 | 6 | 4 | 66.6667 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 88.8889 | 100.0000 | 80.0000 | 79.1667 | 24 | 0 | 24 | 6 | 6 | 100.0000 | |
| dgrover-gatk | INDEL | I6_15 | map_siren | * | 97.1901 | 96.3934 | 98.0000 | 85.1852 | 294 | 11 | 294 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.7964 | 99.6289 | 99.9645 | 66.6982 | 16912 | 63 | 16912 | 6 | 5 | 83.3333 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 97.7836 | 97.1503 | 98.4252 | 91.2111 | 375 | 11 | 375 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 97.6407 | 97.4638 | 97.8182 | 91.2809 | 269 | 7 | 269 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.7964 | 99.6289 | 99.9645 | 66.6982 | 16912 | 63 | 16912 | 6 | 5 | 83.3333 | |
| dgrover-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.9143 | 99.8827 | 99.9458 | 56.3849 | 11071 | 13 | 11067 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.8771 | 100.0000 | 99.7546 | 51.5937 | 2439 | 0 | 2439 | 6 | 0 | 0.0000 | |
| dgrover-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.8105 | 100.0000 | 99.6217 | 53.8819 | 1580 | 0 | 1580 | 6 | 0 | 0.0000 | |
| dgrover-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 99.3818 | 99.2284 | 99.5356 | 87.4927 | 1286 | 10 | 1286 | 6 | 6 | 100.0000 | |
| dgrover-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 99.4131 | 99.5300 | 99.2966 | 88.5687 | 847 | 4 | 847 | 6 | 6 | 100.0000 | |
| dgrover-gatk | SNP | tv | HG002compoundhet | homalt | 99.8671 | 99.9115 | 99.8228 | 42.6879 | 3385 | 3 | 3380 | 6 | 5 | 83.3333 | |
| dgrover-gatk | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.9175 | 99.8900 | 99.9450 | 60.3037 | 10899 | 12 | 10895 | 6 | 5 | 83.3333 | |
| dgrover-gatk | SNP | tv | map_l150_m1_e0 | homalt | 99.4146 | 98.9863 | 99.8466 | 69.3080 | 3906 | 40 | 3906 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | tv | map_l150_m2_e0 | homalt | 99.4343 | 99.0203 | 99.8518 | 71.6158 | 4043 | 40 | 4043 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | tv | map_l150_m2_e1 | homalt | 99.4413 | 99.0324 | 99.8537 | 71.5870 | 4094 | 40 | 4094 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | tv | segdup | homalt | 99.8765 | 99.9382 | 99.8149 | 89.5365 | 3236 | 2 | 3236 | 6 | 6 | 100.0000 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 85.0092 | 76.6467 | 95.4198 | 68.8095 | 128 | 39 | 125 | 6 | 5 | 83.3333 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 80.0000 | 71.2644 | 91.1765 | 99.9005 | 62 | 25 | 62 | 6 | 2 | 33.3333 | |
| egarrison-hhga | INDEL | * | map_l250_m0_e0 | * | 92.9936 | 93.5897 | 92.4051 | 99.7821 | 73 | 5 | 73 | 6 | 1 | 16.6667 | |
| egarrison-hhga | INDEL | * | map_l250_m0_e0 | het | 90.7407 | 92.4528 | 89.0909 | 97.6774 | 49 | 4 | 49 | 6 | 1 | 16.6667 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 85.9341 | 80.4598 | 92.2078 | 71.1610 | 70 | 17 | 71 | 6 | 5 | 83.3333 | |
| ckim-isaac | INDEL | D16_PLUS | map_l100_m1_e0 | * | 35.2996 | 22.9885 | 76.0000 | 91.9094 | 20 | 67 | 19 | 6 | 3 | 50.0000 | |
| ckim-isaac | INDEL | D16_PLUS | map_l100_m1_e0 | het | 26.6667 | 17.3913 | 57.1429 | 93.5484 | 8 | 38 | 8 | 6 | 3 | 50.0000 | |
| ckim-isaac | INDEL | D16_PLUS | map_l100_m2_e0 | * | 35.8056 | 23.3333 | 76.9231 | 92.6346 | 21 | 69 | 20 | 6 | 3 | 50.0000 | |
| ckim-isaac | INDEL | D16_PLUS | map_l100_m2_e0 | het | 28.2353 | 18.7500 | 57.1429 | 94.4444 | 9 | 39 | 8 | 6 | 3 | 50.0000 | |
| ckim-isaac | INDEL | D16_PLUS | map_l100_m2_e1 | * | 37.7178 | 24.7423 | 79.3103 | 92.0330 | 24 | 73 | 23 | 6 | 3 | 50.0000 | |
| ckim-isaac | INDEL | D16_PLUS | map_l100_m2_e1 | het | 29.5567 | 19.6078 | 60.0000 | 94.2085 | 10 | 41 | 9 | 6 | 3 | 50.0000 | |
| ckim-isaac | INDEL | D16_PLUS | segdup | * | 86.7257 | 84.4828 | 89.0909 | 92.1090 | 49 | 9 | 49 | 6 | 3 | 50.0000 | |
| ckim-isaac | INDEL | D16_PLUS | segdup | het | 86.4020 | 89.1892 | 83.7838 | 91.6290 | 33 | 4 | 31 | 6 | 3 | 50.0000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 87.5378 | 78.4574 | 98.9950 | 44.8753 | 590 | 162 | 591 | 6 | 5 | 83.3333 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 87.1765 | 82.4324 | 92.5000 | 74.6032 | 61 | 13 | 74 | 6 | 6 | 100.0000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 82.4610 | 70.7692 | 98.7805 | 27.7533 | 460 | 190 | 486 | 6 | 5 | 83.3333 | |
| ckim-isaac | INDEL | D1_5 | map_l150_m1_e0 | het | 79.8048 | 67.2199 | 98.1873 | 91.0516 | 324 | 158 | 325 | 6 | 2 | 33.3333 | |
| ckim-isaac | INDEL | D1_5 | map_l150_m2_e0 | het | 79.9092 | 67.3152 | 98.3003 | 91.4899 | 346 | 168 | 347 | 6 | 2 | 33.3333 | |