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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
56951-57000 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 89.6000 | 81.1594 | 100.0000 | 52.5424 | 56 | 13 | 56 | 0 | 0 | ||
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 72.7050 | 91.2162 | 60.4396 | 74.6165 | 135 | 13 | 110 | 72 | 71 | 98.6111 | |
| ckim-vqsr | INDEL | D6_15 | map_l100_m2_e1 | * | 95.9707 | 95.2727 | 96.6790 | 89.6919 | 262 | 13 | 262 | 9 | 2 | 22.2222 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 94.0845 | 91.8750 | 96.4029 | 90.0144 | 147 | 13 | 134 | 5 | 4 | 80.0000 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.9112 | 96.6495 | 99.2063 | 75.8157 | 375 | 13 | 375 | 3 | 2 | 66.6667 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 91.6129 | 84.5238 | 100.0000 | 53.8961 | 71 | 13 | 71 | 0 | 0 | ||
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 88.0734 | 78.6885 | 100.0000 | 52.4752 | 48 | 13 | 48 | 0 | 0 | ||
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.7253 | 99.7898 | 99.6609 | 56.0602 | 6171 | 13 | 6171 | 21 | 2 | 9.5238 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.5496 | 99.5667 | 99.5326 | 76.5043 | 2987 | 13 | 2981 | 14 | 4 | 28.5714 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 93.6324 | 98.9002 | 88.8973 | 60.3677 | 1169 | 13 | 1169 | 146 | 145 | 99.3151 | |
| dgrover-gatk | INDEL | * | map_l250_m1_e0 | * | 95.7377 | 95.7377 | 95.7377 | 96.2967 | 292 | 13 | 292 | 13 | 3 | 23.0769 | |
| dgrover-gatk | INDEL | * | map_l250_m2_e0 | * | 96.0725 | 96.0725 | 96.0725 | 96.4988 | 318 | 13 | 318 | 13 | 3 | 23.0769 | |
| dgrover-gatk | INDEL | * | map_l250_m2_e1 | * | 96.0961 | 96.0961 | 96.0961 | 96.5720 | 320 | 13 | 320 | 13 | 3 | 23.0769 | |
| dgrover-gatk | INDEL | * | map_siren | hetalt | 97.0971 | 94.7368 | 99.5781 | 87.1266 | 234 | 13 | 236 | 1 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m1_e0 | het | 98.6818 | 98.9247 | 98.4401 | 85.0991 | 1196 | 13 | 1199 | 19 | 3 | 15.7895 | |
| dgrover-gatk | INDEL | D1_5 | map_l150_m2_e1 | * | 98.2053 | 98.3290 | 98.0818 | 90.2929 | 765 | 13 | 767 | 15 | 4 | 26.6667 | |
| ckim-isaac | SNP | ti | tech_badpromoters | * | 91.7197 | 84.7059 | 100.0000 | 34.5455 | 72 | 13 | 72 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.7375 | 99.6412 | 99.8341 | 75.9622 | 3610 | 13 | 3610 | 6 | 3 | 50.0000 | |
| ckim-vqsr | INDEL | * | map_l250_m2_e0 | het | 90.9931 | 93.8095 | 88.3408 | 97.8444 | 197 | 13 | 197 | 26 | 1 | 3.8462 | |
| ckim-vqsr | INDEL | * | map_l250_m2_e1 | het | 91.0345 | 93.8389 | 88.3929 | 97.8943 | 198 | 13 | 198 | 26 | 1 | 3.8462 | |
| dgrover-gatk | INDEL | D6_15 | map_l100_m2_e1 | * | 96.1468 | 95.2727 | 97.0370 | 87.9086 | 262 | 13 | 262 | 8 | 2 | 25.0000 | |
| dgrover-gatk | INDEL | D6_15 | map_siren | * | 97.7320 | 97.4460 | 98.0198 | 85.5879 | 496 | 13 | 495 | 10 | 2 | 20.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l100_m1_e0 | het | 98.7103 | 98.3269 | 99.0968 | 85.3053 | 764 | 13 | 768 | 7 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l100_m2_e0 | het | 98.7364 | 98.3607 | 99.1150 | 86.3291 | 780 | 13 | 784 | 7 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l100_m2_e1 | het | 98.7630 | 98.3951 | 99.1337 | 86.3950 | 797 | 13 | 801 | 7 | 0 | 0.0000 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.5351 | 99.4510 | 99.6193 | 87.6224 | 2355 | 13 | 2355 | 9 | 9 | 100.0000 | |
| 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 | * | map_l250_m0_e0 | homalt | 98.5600 | 97.9332 | 99.1948 | 91.6845 | 616 | 13 | 616 | 5 | 3 | 60.0000 | |
| dgrover-gatk | SNP | * | segdup | homalt | 99.8976 | 99.8790 | 99.9162 | 88.2042 | 10730 | 13 | 10730 | 9 | 9 | 100.0000 | |
| dgrover-gatk | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.3391 | 99.1425 | 99.5364 | 69.3276 | 1503 | 13 | 1503 | 7 | 2 | 28.5714 | |
| egarrison-hhga | INDEL | * | map_l250_m1_e0 | * | 96.0526 | 95.7377 | 96.3696 | 99.5069 | 292 | 13 | 292 | 11 | 3 | 27.2727 | |
| egarrison-hhga | INDEL | * | map_l250_m2_e0 | * | 96.3636 | 96.0725 | 96.6565 | 99.5239 | 318 | 13 | 318 | 11 | 3 | 27.2727 | |
| egarrison-hhga | INDEL | * | map_l250_m2_e1 | * | 96.3855 | 96.0961 | 96.6767 | 99.5385 | 320 | 13 | 320 | 11 | 3 | 27.2727 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 64.8649 | 48.0000 | 100.0000 | 45.8333 | 12 | 13 | 13 | 0 | 0 | ||
| egarrison-hhga | INDEL | D1_5 | map_l100_m0_e0 | het | 97.4705 | 97.8003 | 97.1429 | 84.6491 | 578 | 13 | 578 | 17 | 3 | 17.6471 | |
| egarrison-hhga | INDEL | D1_5 | map_l100_m1_e0 | hetalt | 82.8962 | 72.3404 | 97.0588 | 92.0188 | 34 | 13 | 33 | 1 | 1 | 100.0000 | |
| egarrison-hhga | INDEL | D1_5 | map_l100_m2_e0 | hetalt | 83.3042 | 72.9167 | 97.1429 | 92.3077 | 35 | 13 | 34 | 1 | 1 | 100.0000 | |
| egarrison-hhga | INDEL | D1_5 | map_l100_m2_e1 | hetalt | 84.4191 | 74.5098 | 97.3684 | 91.9149 | 38 | 13 | 37 | 1 | 1 | 100.0000 | |
| egarrison-hhga | INDEL | D1_5 | map_l125_m1_e0 | het | 98.0069 | 98.2094 | 97.8052 | 85.5214 | 713 | 13 | 713 | 16 | 3 | 18.7500 | |
| egarrison-hhga | INDEL | D1_5 | map_l125_m2_e0 | het | 98.1058 | 98.2984 | 97.9140 | 86.2050 | 751 | 13 | 751 | 16 | 3 | 18.7500 | |
| egarrison-hhga | INDEL | D1_5 | map_l125_m2_e1 | het | 98.0570 | 98.3117 | 97.8036 | 86.2863 | 757 | 13 | 757 | 17 | 4 | 23.5294 | |
| egarrison-hhga | INDEL | I1_5 | map_l100_m2_e1 | het | 98.5167 | 98.3951 | 98.6386 | 85.2231 | 797 | 13 | 797 | 11 | 1 | 9.0909 | |
| egarrison-hhga | INDEL | I1_5 | segdup | * | 98.8191 | 98.7724 | 98.8658 | 94.3109 | 1046 | 13 | 1046 | 12 | 6 | 50.0000 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 90.0691 | 91.5033 | 88.6792 | 75.9091 | 140 | 13 | 141 | 18 | 12 | 66.6667 | |
| egarrison-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | * | 97.9455 | 96.8900 | 99.0244 | 46.7532 | 405 | 13 | 406 | 4 | 4 | 100.0000 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 99.2393 | 99.5160 | 98.9641 | 59.7528 | 2673 | 13 | 2675 | 28 | 4 | 14.2857 | |
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 99.5478 | 99.4890 | 99.6066 | 49.0683 | 2531 | 13 | 2532 | 10 | 2 | 20.0000 | |
| egarrison-hhga | SNP | ti | map_l250_m1_e0 | homalt | 99.5006 | 99.1910 | 99.8121 | 86.3830 | 1594 | 13 | 1594 | 3 | 3 | 100.0000 | |
| egarrison-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 93.2878 | 89.5161 | 97.3913 | 86.9615 | 111 | 13 | 112 | 3 | 1 | 33.3333 | |
| egarrison-hhga | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.7811 | 99.6656 | 99.8969 | 59.9463 | 3874 | 13 | 3874 | 4 | 4 | 100.0000 | |