PrecisionFDA
Truth Challenge
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
30551-30600 / 86044 show all | |||||||||||||||
| ckim-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 96.9697 | 100.0000 | 94.1176 | 88.1119 | 52 | 0 | 48 | 3 | 0 | 0.0000 | |
| mlin-fermikit | INDEL | D1_5 | map_siren | hetalt | 75.5556 | 60.7143 | 100.0000 | 88.1119 | 51 | 33 | 51 | 0 | 0 | ||
| rpoplin-dv42 | SNP | * | map_l250_m2_e0 | het | 98.1499 | 98.0554 | 98.2446 | 88.1117 | 5093 | 101 | 5093 | 91 | 56 | 61.5385 | |
| hfeng-pmm3 | SNP | tv | map_l250_m2_e1 | homalt | 99.3671 | 99.5772 | 99.1579 | 88.1116 | 942 | 4 | 942 | 8 | 4 | 50.0000 | |
| gduggal-bwavard | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 82.0661 | 89.3056 | 75.9124 | 88.1111 | 643 | 77 | 624 | 198 | 59 | 29.7980 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | het | 53.3937 | 39.8649 | 80.8219 | 88.1107 | 59 | 89 | 59 | 14 | 7 | 50.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | map_l150_m2_e0 | homalt | 99.3789 | 99.1736 | 99.5851 | 88.1105 | 240 | 2 | 240 | 1 | 1 | 100.0000 | |
| jpowers-varprowl | INDEL | I6_15 | map_l100_m2_e0 | het | 71.7949 | 68.8525 | 75.0000 | 88.1104 | 42 | 19 | 42 | 14 | 14 | 100.0000 | |
| rpoplin-dv42 | INDEL | * | map_l150_m1_e0 | homalt | 98.7013 | 98.7013 | 98.7013 | 88.1081 | 456 | 6 | 456 | 6 | 5 | 83.3333 | |
| rpoplin-dv42 | SNP | tv | map_l250_m2_e1 | homalt | 98.2869 | 97.0402 | 99.5662 | 88.1078 | 918 | 28 | 918 | 4 | 4 | 100.0000 | |
| qzeng-custom | INDEL | I1_5 | map_l150_m2_e0 | homalt | 75.8531 | 61.6915 | 98.4536 | 88.1055 | 124 | 77 | 191 | 3 | 2 | 66.6667 | |
| ckim-gatk | INDEL | D1_5 | map_l150_m1_e0 | homalt | 99.1189 | 98.6842 | 99.5575 | 88.1053 | 225 | 3 | 225 | 1 | 1 | 100.0000 | |
| ckim-vqsr | INDEL | D1_5 | map_l150_m1_e0 | homalt | 99.1189 | 98.6842 | 99.5575 | 88.1053 | 225 | 3 | 225 | 1 | 1 | 100.0000 | |
| gduggal-bwaplat | SNP | ti | map_l125_m1_e0 | het | 79.9258 | 66.9495 | 99.1416 | 88.1040 | 12229 | 6037 | 12243 | 106 | 30 | 28.3019 | |
| ciseli-custom | INDEL | D6_15 | map_l100_m0_e0 | homalt | 55.7377 | 70.8333 | 45.9459 | 88.1029 | 17 | 7 | 17 | 20 | 19 | 95.0000 | |
| gduggal-snapvard | SNP | tv | map_l250_m2_e0 | homalt | 96.5358 | 93.7033 | 99.5449 | 88.1007 | 878 | 59 | 875 | 4 | 2 | 50.0000 | |
| ckim-dragen | INDEL | D1_5 | map_l150_m2_e0 | homalt | 98.9596 | 98.3471 | 99.5798 | 88.1000 | 238 | 4 | 237 | 1 | 1 | 100.0000 | |
| rpoplin-dv42 | INDEL | D1_5 | map_l125_m0_e0 | * | 97.8830 | 97.7823 | 97.9839 | 88.0998 | 485 | 11 | 486 | 10 | 4 | 40.0000 | |
| gduggal-bwafb | SNP | ti | map_l250_m1_e0 | homalt | 98.9956 | 98.1332 | 99.8733 | 88.0983 | 1577 | 30 | 1577 | 2 | 2 | 100.0000 | |
| ltrigg-rtg1 | SNP | * | segdup | * | 99.0787 | 99.6188 | 98.5445 | 88.0967 | 27960 | 107 | 27963 | 413 | 51 | 12.3487 | |
| ltrigg-rtg1 | INDEL | C6_15 | HG002compoundhet | het | 0.0000 | 0.0000 | 95.0000 | 88.0952 | 0 | 0 | 19 | 1 | 0 | 0.0000 | |
| jli-custom | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 90.9091 | 83.3333 | 100.0000 | 88.0952 | 5 | 1 | 5 | 0 | 0 | ||
| jmaeng-gatk | INDEL | * | map_l100_m2_e0 | hetalt | 92.7039 | 86.4000 | 100.0000 | 88.0952 | 108 | 17 | 110 | 0 | 0 | ||
| rpoplin-dv42 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 33.3333 | 100.0000 | 20.0000 | 88.0952 | 1 | 0 | 1 | 4 | 3 | 75.0000 | |
| raldana-dualsentieon | SNP | * | map_l250_m2_e1 | hetalt | 100.0000 | 100.0000 | 100.0000 | 88.0952 | 5 | 0 | 5 | 0 | 0 | ||
| raldana-dualsentieon | SNP | tv | map_l250_m2_e1 | hetalt | 100.0000 | 100.0000 | 100.0000 | 88.0952 | 5 | 0 | 5 | 0 | 0 | ||
| qzeng-custom | SNP | ti | map_l100_m1_e0 | hetalt | 81.6327 | 68.9655 | 100.0000 | 88.0952 | 20 | 9 | 20 | 0 | 0 | ||
| mlin-fermikit | INDEL | I16_PLUS | map_l150_m2_e0 | het | 72.7273 | 66.6667 | 80.0000 | 88.0952 | 4 | 2 | 4 | 1 | 1 | 100.0000 | |
| mlin-fermikit | INDEL | I16_PLUS | map_l150_m2_e1 | het | 72.7273 | 66.6667 | 80.0000 | 88.0952 | 4 | 2 | 4 | 1 | 1 | 100.0000 | |
| ciseli-custom | INDEL | * | map_l100_m2_e1 | * | 70.6710 | 66.2407 | 75.7364 | 88.0952 | 2488 | 1268 | 2494 | 799 | 531 | 66.4581 | |
| ckim-gatk | INDEL | I16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 93.3333 | 93.3333 | 93.3333 | 88.0952 | 14 | 1 | 14 | 1 | 0 | 0.0000 | |
| gduggal-bwafb | SNP | ti | map_l250_m2_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 88.0952 | 5 | 0 | 5 | 0 | 0 | ||
| gduggal-bwafb | SNP | ti | map_l250_m2_e1 | hetalt | 100.0000 | 100.0000 | 100.0000 | 88.0952 | 5 | 0 | 5 | 0 | 0 | ||
| eyeh-varpipe | SNP | tv | map_l250_m2_e1 | hetalt | 97.4359 | 100.0000 | 95.0000 | 88.0952 | 5 | 0 | 19 | 1 | 0 | 0.0000 | |
| cchapple-custom | INDEL | C16_PLUS | HG002complexvar | homalt | 0.0000 | 0.0000 | 100.0000 | 88.0952 | 0 | 0 | 20 | 0 | 0 | ||
| hfeng-pmm3 | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 90.9091 | 83.3333 | 100.0000 | 88.0952 | 5 | 1 | 5 | 0 | 0 | ||
| ckim-dragen | INDEL | * | map_l150_m1_e0 | homalt | 98.4759 | 98.0519 | 98.9035 | 88.0940 | 453 | 9 | 451 | 5 | 4 | 80.0000 | |
| anovak-vg | INDEL | * | map_l150_m2_e0 | homalt | 76.2649 | 84.1996 | 69.6970 | 88.0938 | 405 | 76 | 414 | 180 | 160 | 88.8889 | |
| ndellapenna-hhga | SNP | ti | map_l250_m1_e0 | het | 97.6313 | 95.8221 | 99.5101 | 88.0937 | 2844 | 124 | 2844 | 14 | 6 | 42.8571 | |
| gduggal-bwafb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 81.4625 | 93.8889 | 71.9409 | 88.0905 | 676 | 44 | 682 | 266 | 37 | 13.9098 | |
| jlack-gatk | INDEL | * | map_l100_m2_e1 | hetalt | 92.3109 | 86.3636 | 99.1379 | 88.0903 | 114 | 18 | 115 | 1 | 0 | 0.0000 | |
| rpoplin-dv42 | SNP | * | map_l250_m2_e1 | * | 98.3291 | 97.9967 | 98.6638 | 88.0879 | 7827 | 160 | 7827 | 106 | 70 | 66.0377 | |
| astatham-gatk | INDEL | D1_5 | map_l125_m2_e1 | * | 96.9505 | 96.1106 | 97.8051 | 88.0870 | 1112 | 45 | 1114 | 25 | 5 | 20.0000 | |
| ltrigg-rtg2 | INDEL | C1_5 | HG002complexvar | * | 91.9145 | 85.7143 | 99.0816 | 88.0866 | 6 | 1 | 971 | 9 | 3 | 33.3333 | |
| rpoplin-dv42 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.3720 | 99.7481 | 98.9987 | 88.0853 | 792 | 2 | 791 | 8 | 6 | 75.0000 | |
| asubramanian-gatk | SNP | * | map_l125_m2_e1 | homalt | 42.1801 | 26.7283 | 99.9787 | 88.0838 | 4686 | 12846 | 4686 | 1 | 0 | 0.0000 | |
| gduggal-snapvard | SNP | * | map_l250_m2_e1 | homalt | 96.5507 | 93.7822 | 99.4876 | 88.0830 | 2549 | 169 | 2524 | 13 | 9 | 69.2308 | |
| hfeng-pmm3 | SNP | tv | map_l250_m1_e0 | het | 98.3966 | 97.8735 | 98.9253 | 88.0822 | 1749 | 38 | 1749 | 19 | 0 | 0.0000 | |
| gduggal-snapvard | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 90.3824 | 85.7143 | 95.5882 | 88.0806 | 402 | 67 | 390 | 18 | 8 | 44.4444 | |
| gduggal-snapvard | SNP | ti | map_l250_m2_e1 | homalt | 96.5718 | 93.8488 | 99.4575 | 88.0802 | 1663 | 109 | 1650 | 9 | 7 | 77.7778 | |