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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
63001-63050 / 86044 show all | |||||||||||||||
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 95.9027 | 95.4955 | 96.3134 | 65.1685 | 212 | 10 | 209 | 8 | 5 | 62.5000 | |
| dgrover-gatk | INDEL | * | map_l100_m0_e0 | homalt | 98.1391 | 98.4283 | 97.8516 | 85.3798 | 501 | 8 | 501 | 11 | 5 | 45.4545 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.9231 | 96.3983 | 99.4970 | 32.4728 | 910 | 34 | 989 | 5 | 5 | 100.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 96.8861 | 95.1429 | 98.6945 | 35.5219 | 333 | 17 | 378 | 5 | 5 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.4819 | 99.6109 | 99.3532 | 78.1854 | 1536 | 6 | 1536 | 10 | 5 | 50.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.0410 | 89.1557 | 99.4928 | 31.2609 | 1151 | 140 | 1177 | 6 | 5 | 83.3333 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.9319 | 100.0000 | 99.8638 | 51.2807 | 3666 | 0 | 3666 | 5 | 5 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m1_e0 | * | 98.8105 | 98.8095 | 98.8115 | 84.8192 | 1826 | 22 | 1829 | 22 | 5 | 22.7273 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m2_e0 | * | 98.8260 | 98.7990 | 98.8530 | 85.3498 | 1892 | 23 | 1896 | 22 | 5 | 22.7273 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m2_e1 | * | 98.8405 | 98.8138 | 98.8671 | 85.4314 | 1916 | 23 | 1920 | 22 | 5 | 22.7273 | |
| dgrover-gatk | INDEL | D1_5 | map_siren | * | 99.2924 | 99.2916 | 99.2932 | 82.3565 | 3504 | 25 | 3512 | 25 | 5 | 20.0000 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 95.1611 | 91.0564 | 99.6533 | 48.4903 | 3146 | 309 | 3162 | 11 | 5 | 45.4545 | |
| ckim-isaac | SNP | * | map_l125_m0_e0 | * | 70.7547 | 54.8207 | 99.7466 | 75.5092 | 10627 | 8758 | 10627 | 27 | 5 | 18.5185 | |
| ckim-isaac | SNP | * | map_l125_m1_e0 | homalt | 66.8137 | 50.1804 | 99.9411 | 61.4585 | 8483 | 8422 | 8483 | 5 | 5 | 100.0000 | |
| ckim-isaac | SNP | * | map_l125_m2_e0 | homalt | 67.3485 | 50.7856 | 99.9434 | 65.6165 | 8824 | 8551 | 8824 | 5 | 5 | 100.0000 | |
| ckim-isaac | SNP | * | map_l150_m2_e1 | homalt | 63.8200 | 46.8842 | 99.9099 | 70.9059 | 5545 | 6282 | 5545 | 5 | 5 | 100.0000 | |
| ckim-isaac | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 91.7019 | 85.8108 | 98.4615 | 77.2063 | 381 | 63 | 384 | 6 | 5 | 83.3333 | |
| ckim-isaac | SNP | ti | map_l100_m1_e0 | homalt | 75.0391 | 60.0668 | 99.9537 | 52.8051 | 10788 | 7172 | 10788 | 5 | 5 | 100.0000 | |
| ckim-isaac | SNP | ti | map_l100_m2_e0 | homalt | 75.4234 | 60.5604 | 99.9549 | 56.7558 | 11088 | 7221 | 11088 | 5 | 5 | 100.0000 | |
| ckim-isaac | SNP | ti | map_l100_m2_e1 | homalt | 75.4653 | 60.6143 | 99.9554 | 56.7172 | 11210 | 7284 | 11210 | 5 | 5 | 100.0000 | |
| ckim-isaac | SNP | ti | map_l150_m1_e0 | * | 71.6515 | 55.9050 | 99.7466 | 75.8793 | 11020 | 8692 | 11020 | 28 | 5 | 17.8571 | |
| ckim-isaac | SNP | ti | map_l150_m2_e0 | * | 72.1859 | 56.5571 | 99.7506 | 77.5984 | 11601 | 8911 | 11601 | 29 | 5 | 17.2414 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 95.2859 | 91.1304 | 99.8384 | 63.0944 | 4942 | 481 | 4944 | 8 | 5 | 62.5000 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 95.2859 | 91.1304 | 99.8384 | 63.0944 | 4942 | 481 | 4944 | 8 | 5 | 62.5000 | |
| ckim-isaac | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 96.6143 | 93.9646 | 99.4178 | 33.0736 | 4406 | 283 | 4440 | 26 | 5 | 19.2308 | |
| ckim-isaac | SNP | tv | lowcmp_SimpleRepeat_quadTR_51to200 | * | 66.1640 | 61.9048 | 71.0526 | 87.6623 | 26 | 16 | 27 | 11 | 5 | 45.4545 | |
| ckim-isaac | SNP | tv | map_siren | homalt | 77.1855 | 62.8654 | 99.9539 | 50.4637 | 10838 | 6402 | 10838 | 5 | 5 | 100.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7617 | 99.8940 | 99.6298 | 72.7247 | 1884 | 2 | 1884 | 7 | 5 | 71.4286 | |
| ckim-vqsr | INDEL | * | map_l100_m1_e0 | homalt | 99.2254 | 99.1850 | 99.2659 | 84.2639 | 1217 | 10 | 1217 | 9 | 5 | 55.5556 | |
| ckim-vqsr | INDEL | * | map_l100_m2_e0 | homalt | 99.2070 | 99.2070 | 99.2070 | 85.1821 | 1251 | 10 | 1251 | 10 | 5 | 50.0000 | |
| ckim-vqsr | INDEL | * | map_l100_m2_e1 | homalt | 99.2194 | 99.2194 | 99.2194 | 85.2079 | 1271 | 10 | 1271 | 10 | 5 | 50.0000 | |
| ckim-vqsr | INDEL | * | map_l125_m1_e0 | het | 95.6747 | 95.2060 | 96.1480 | 92.4743 | 1271 | 64 | 1273 | 51 | 5 | 9.8039 | |
| ckim-vqsr | INDEL | * | map_l125_m2_e0 | het | 95.6234 | 94.9676 | 96.2882 | 93.0044 | 1321 | 70 | 1323 | 51 | 5 | 9.8039 | |
| ckim-vqsr | INDEL | * | map_l125_m2_e1 | het | 95.6019 | 94.8864 | 96.3283 | 93.0623 | 1336 | 72 | 1338 | 51 | 5 | 9.8039 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.8135 | 96.1864 | 99.4965 | 31.6116 | 908 | 36 | 988 | 5 | 5 | 100.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.3534 | 99.7835 | 98.9270 | 64.3185 | 461 | 1 | 461 | 5 | 5 | 100.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.8792 | 99.4987 | 98.2673 | 65.6463 | 397 | 2 | 397 | 7 | 5 | 71.4286 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 96.7378 | 94.8571 | 98.6945 | 34.1924 | 332 | 18 | 378 | 5 | 5 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.5135 | 99.4812 | 99.5457 | 78.2406 | 1534 | 8 | 1534 | 7 | 5 | 71.4286 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 93.3378 | 87.8389 | 99.5712 | 29.6743 | 1134 | 157 | 1161 | 5 | 5 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_l125_m1_e0 | * | 96.7371 | 96.6912 | 96.7831 | 90.6738 | 1052 | 36 | 1053 | 35 | 5 | 14.2857 | |
| ckim-vqsr | INDEL | D1_5 | map_l125_m2_e0 | * | 96.7133 | 96.5004 | 96.9271 | 91.1664 | 1103 | 40 | 1104 | 35 | 5 | 14.2857 | |
| ckim-vqsr | INDEL | D1_5 | map_l125_m2_e1 | * | 96.7084 | 96.4564 | 96.9618 | 91.2142 | 1116 | 41 | 1117 | 35 | 5 | 14.2857 | |
| ckim-vqsr | INDEL | D1_5 | map_l150_m2_e1 | * | 95.8895 | 95.8869 | 95.8922 | 92.8591 | 746 | 32 | 747 | 32 | 5 | 15.6250 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.4656 | 94.7248 | 98.2716 | 85.9667 | 413 | 23 | 398 | 7 | 5 | 71.4286 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 96.6974 | 95.4955 | 97.9299 | 88.5024 | 636 | 30 | 615 | 13 | 5 | 38.4615 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 89.7959 | 100.0000 | 81.4815 | 87.3832 | 22 | 0 | 22 | 5 | 5 | 100.0000 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 96.6974 | 95.4955 | 97.9299 | 88.5024 | 636 | 30 | 615 | 13 | 5 | 38.4615 | |
| ckim-vqsr | INDEL | I1_5 | * | hetalt | 95.5907 | 91.5945 | 99.9516 | 60.1444 | 10254 | 941 | 10316 | 5 | 5 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.5020 | 96.0317 | 99.0180 | 65.9610 | 605 | 25 | 605 | 6 | 5 | 83.3333 | |