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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
68951-69000 / 86044 show all | |||||||||||||||
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.1904 | 98.9943 | 97.3994 | 67.4787 | 14470 | 147 | 14082 | 376 | 350 | 93.0851 | |
| hfeng-pmm1 | INDEL | * | map_l100_m2_e1 | * | 98.1906 | 97.4707 | 98.9213 | 83.6789 | 3661 | 95 | 3668 | 40 | 9 | 22.5000 | |
| ndellapenna-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.1911 | 97.7409 | 98.6454 | 80.0759 | 10557 | 244 | 10559 | 145 | 73 | 50.3448 | |
| bgallagher-sentieon | SNP | tv | map_l250_m0_e0 | homalt | 98.1912 | 98.4456 | 97.9381 | 92.2400 | 190 | 3 | 190 | 4 | 3 | 75.0000 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 98.1914 | 99.7899 | 96.6433 | 56.0900 | 9501 | 20 | 9501 | 330 | 327 | 99.0909 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.1915 | 97.4975 | 98.8955 | 61.4377 | 30622 | 786 | 30622 | 342 | 309 | 90.3509 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.1915 | 97.4975 | 98.8955 | 61.4377 | 30622 | 786 | 30622 | 342 | 309 | 90.3509 | |
| dgrover-gatk | INDEL | D1_5 | map_l150_m1_e0 | * | 98.1921 | 98.3264 | 98.0583 | 89.8594 | 705 | 12 | 707 | 14 | 3 | 21.4286 | |
| ciseli-custom | SNP | ti | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 98.1931 | 99.5911 | 96.8338 | 44.7388 | 2192 | 9 | 2202 | 72 | 34 | 47.2222 | |
| cchapple-custom | SNP | ti | map_l150_m2_e1 | homalt | 98.1938 | 96.4643 | 99.9865 | 68.8251 | 7421 | 272 | 7418 | 1 | 1 | 100.0000 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.1938 | 98.9533 | 97.4458 | 67.6938 | 14464 | 153 | 14078 | 369 | 346 | 93.7669 | |
| mlin-fermikit | SNP | ti | HG002complexvar | het | 98.1941 | 96.4761 | 99.9743 | 15.7268 | 303674 | 11092 | 303641 | 78 | 14 | 17.9487 | |
| hfeng-pmm3 | INDEL | * | map_l150_m2_e1 | * | 98.1943 | 98.1237 | 98.2651 | 88.7746 | 1412 | 27 | 1416 | 25 | 6 | 24.0000 | |
| jli-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.1944 | 96.7449 | 99.6880 | 59.3016 | 1278 | 43 | 1278 | 4 | 3 | 75.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.1949 | 97.6719 | 98.7235 | 54.4572 | 21732 | 518 | 21733 | 281 | 265 | 94.3060 | |
| ckim-vqsr | INDEL | I16_PLUS | * | het | 98.1949 | 97.2774 | 99.1298 | 76.5400 | 2644 | 74 | 2620 | 23 | 10 | 43.4783 | |
| hfeng-pmm3 | INDEL | * | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.1954 | 96.9884 | 99.4328 | 50.3319 | 35490 | 1102 | 35413 | 202 | 180 | 89.1089 | |
| jmaeng-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.1956 | 99.3209 | 97.0954 | 73.3937 | 1170 | 8 | 1170 | 35 | 35 | 100.0000 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.1963 | 97.6190 | 98.7805 | 79.4486 | 164 | 4 | 162 | 2 | 1 | 50.0000 | |
| raldana-dualsentieon | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.1964 | 99.5935 | 96.8379 | 59.5200 | 490 | 2 | 490 | 16 | 15 | 93.7500 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.1965 | 97.0144 | 99.4078 | 64.7466 | 15597 | 480 | 15611 | 93 | 72 | 77.4194 | |
| jli-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.1965 | 97.0144 | 99.4078 | 64.7466 | 15597 | 480 | 15611 | 93 | 72 | 77.4194 | |
| mlin-fermikit | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.1967 | 97.8663 | 98.5292 | 39.4229 | 7293 | 159 | 7302 | 109 | 85 | 77.9817 | |
| hfeng-pmm3 | INDEL | I16_PLUS | * | homalt | 98.1968 | 99.4234 | 97.0000 | 68.6397 | 1552 | 9 | 1552 | 48 | 45 | 93.7500 | |
| gduggal-bwafb | INDEL | I1_5 | segdup | * | 98.1968 | 97.6393 | 98.7607 | 94.3611 | 1034 | 25 | 1036 | 13 | 6 | 46.1538 | |
| gduggal-bwafb | SNP | * | map_l150_m1_e0 | het | 98.1968 | 98.3951 | 97.9994 | 78.1832 | 19006 | 310 | 19006 | 388 | 96 | 24.7423 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 98.1969 | 98.0419 | 98.3525 | 52.6692 | 10865 | 217 | 10865 | 182 | 178 | 97.8022 | |
| rpoplin-dv42 | INDEL | I1_5 | map_l100_m2_e1 | het | 98.1972 | 97.4074 | 99.0000 | 84.3750 | 789 | 21 | 792 | 8 | 5 | 62.5000 | |
| raldana-dualsentieon | INDEL | D1_5 | map_l100_m0_e0 | * | 98.1974 | 97.7984 | 98.5998 | 82.9317 | 844 | 19 | 845 | 12 | 3 | 25.0000 | |
| gduggal-bwavard | SNP | * | segdup | het | 98.1974 | 97.4649 | 98.9410 | 94.6418 | 16878 | 439 | 16724 | 179 | 23 | 12.8492 | |
| jpowers-varprowl | SNP | ti | map_l250_m1_e0 | homalt | 98.1979 | 96.6397 | 99.8072 | 88.8547 | 1553 | 54 | 1553 | 3 | 3 | 100.0000 | |
| ghariani-varprowl | SNP | ti | map_l250_m1_e0 | homalt | 98.1979 | 96.6397 | 99.8072 | 87.4354 | 1553 | 54 | 1553 | 3 | 3 | 100.0000 | |
| gduggal-snapvard | SNP | ti | HG002complexvar | homalt | 98.1979 | 96.6107 | 99.8382 | 17.7966 | 186907 | 6557 | 182591 | 296 | 181 | 61.1486 | |
| ghariani-varprowl | SNP | tv | map_l125_m0_e0 | homalt | 98.1984 | 96.9383 | 99.4917 | 74.3206 | 2153 | 68 | 2153 | 11 | 4 | 36.3636 | |
| jlack-gatk | INDEL | D6_15 | * | homalt | 98.1988 | 99.5416 | 96.8918 | 51.5867 | 6297 | 29 | 6297 | 202 | 199 | 98.5149 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.1989 | 99.8938 | 96.5606 | 60.0492 | 3762 | 4 | 3762 | 134 | 131 | 97.7612 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.1989 | 99.8938 | 96.5606 | 60.0492 | 3762 | 4 | 3762 | 134 | 131 | 97.7612 | |
| raldana-dualsentieon | INDEL | D1_5 | map_l125_m2_e0 | * | 98.1990 | 97.7253 | 98.6772 | 85.2305 | 1117 | 26 | 1119 | 15 | 4 | 26.6667 | |
| asubramanian-gatk | SNP | ti | segdup | * | 98.1992 | 96.8521 | 99.5842 | 91.3917 | 18922 | 615 | 18920 | 79 | 8 | 10.1266 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.1994 | 99.9203 | 96.5367 | 59.9507 | 3763 | 3 | 3763 | 135 | 133 | 98.5185 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.1994 | 99.4197 | 97.0087 | 68.4176 | 3255 | 19 | 3243 | 100 | 97 | 97.0000 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.1994 | 99.9203 | 96.5367 | 59.9507 | 3763 | 3 | 3763 | 135 | 133 | 98.5185 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.1995 | 96.8094 | 99.6302 | 71.4676 | 15080 | 497 | 15087 | 56 | 47 | 83.9286 | |
| jlack-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.1997 | 98.5761 | 97.8261 | 89.4229 | 900 | 13 | 900 | 20 | 13 | 65.0000 | |
| jlack-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.1998 | 96.4633 | 100.0000 | 41.4933 | 1091 | 40 | 1097 | 0 | 0 | ||
| hfeng-pmm2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 98.1998 | 96.7133 | 99.7327 | 79.6799 | 10446 | 355 | 10447 | 28 | 3 | 10.7143 | |
| ltrigg-rtg2 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 98.2000 | 97.2028 | 99.2178 | 83.0336 | 2641 | 76 | 2537 | 20 | 1 | 5.0000 | |
| egarrison-hhga | SNP | tv | HG002compoundhet | het | 98.2001 | 96.8971 | 99.5386 | 52.4849 | 4528 | 145 | 4530 | 21 | 10 | 47.6190 | |
| gduggal-bwavard | SNP | * | lowcmp_SimpleRepeat_triTR_11to50 | * | 98.2001 | 97.4711 | 98.9400 | 41.0943 | 7169 | 186 | 7094 | 76 | 20 | 26.3158 | |
| gduggal-bwafb | SNP | tv | map_l125_m2_e0 | het | 98.2005 | 98.7742 | 97.6335 | 76.4784 | 10314 | 128 | 10314 | 250 | 45 | 18.0000 | |