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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
20001-20050 / 86044 show all | |||||||||||||||
| bgallagher-sentieon | SNP | ti | map_l150_m0_e0 | het | 98.4386 | 98.9798 | 97.9033 | 83.1082 | 5045 | 52 | 5043 | 108 | 15 | 13.8889 | |
| bgallagher-sentieon | SNP | ti | map_l250_m2_e1 | * | 98.6646 | 98.9756 | 98.3555 | 89.6132 | 5024 | 52 | 5024 | 84 | 19 | 22.6190 | |
| bgallagher-sentieon | SNP | tv | HG002complexvar | homalt | 99.9663 | 99.9453 | 99.9874 | 22.7972 | 95059 | 52 | 95044 | 12 | 10 | 83.3333 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.8000 | 99.6479 | 99.9525 | 54.9426 | 14718 | 52 | 14720 | 7 | 1 | 14.2857 | |
| astatham-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 98.9667 | 98.0640 | 99.8862 | 50.8114 | 2634 | 52 | 2634 | 3 | 0 | 0.0000 | |
| astatham-gatk | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.3998 | 98.8910 | 99.9138 | 41.4542 | 4637 | 52 | 4634 | 4 | 1 | 25.0000 | |
| asubramanian-gatk | INDEL | * | map_l125_m1_e0 | homalt | 96.1134 | 92.8962 | 99.5614 | 86.8865 | 680 | 52 | 681 | 3 | 1 | 33.3333 | |
| asubramanian-gatk | INDEL | * | map_l250_m2_e0 | * | 86.7966 | 84.2900 | 89.4569 | 99.1194 | 279 | 52 | 280 | 33 | 3 | 9.0909 | |
| raldana-dualsentieon | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.1576 | 94.7581 | 99.6819 | 66.9239 | 940 | 52 | 940 | 3 | 1 | 33.3333 | |
| rpoplin-dv42 | INDEL | * | map_l125_m2_e0 | * | 98.0800 | 97.6321 | 98.5321 | 98.7156 | 2144 | 52 | 2148 | 32 | 13 | 40.6250 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.3240 | 95.7792 | 96.8750 | 60.5835 | 1180 | 52 | 1178 | 38 | 26 | 68.4211 | |
| rpoplin-dv42 | INDEL | I16_PLUS | HG002complexvar | hetalt | 91.5858 | 84.4776 | 100.0000 | 64.2417 | 283 | 52 | 290 | 0 | 0 | ||
| hfeng-pmm2 | SNP | * | segdup | * | 99.6762 | 99.8147 | 99.5380 | 90.2632 | 28015 | 52 | 28009 | 130 | 13 | 10.0000 | |
| hfeng-pmm2 | SNP | tv | * | homalt | 99.9869 | 99.9862 | 99.9875 | 20.9465 | 377071 | 52 | 377066 | 47 | 24 | 51.0638 | |
| hfeng-pmm3 | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 97.6820 | 95.7792 | 99.6619 | 56.9975 | 1180 | 52 | 1179 | 4 | 3 | 75.0000 | |
| hfeng-pmm3 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 88.5375 | 81.1594 | 97.3913 | 91.0784 | 224 | 52 | 224 | 6 | 0 | 0.0000 | |
| jlack-gatk | INDEL | * | HG002complexvar | homalt | 99.5756 | 99.8076 | 99.3448 | 56.8540 | 26975 | 52 | 26988 | 178 | 171 | 96.0674 | |
| hfeng-pmm1 | INDEL | D1_5 | HG002complexvar | hetalt | 97.9678 | 96.1538 | 99.8514 | 73.2565 | 1300 | 52 | 1344 | 2 | 1 | 50.0000 | |
| hfeng-pmm1 | SNP | ti | map_l250_m1_e0 | * | 98.9508 | 98.8644 | 99.0374 | 88.1947 | 4527 | 52 | 4527 | 44 | 10 | 22.7273 | |
| hfeng-pmm1 | SNP | ti | map_l250_m2_e0 | * | 99.0408 | 98.9617 | 99.1200 | 88.5996 | 4956 | 52 | 4956 | 44 | 10 | 22.7273 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.2948 | 99.3780 | 99.2118 | 59.1033 | 8308 | 52 | 8308 | 66 | 66 | 100.0000 | |
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.2948 | 99.3780 | 99.2118 | 59.1033 | 8308 | 52 | 8308 | 66 | 66 | 100.0000 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 97.8835 | 96.7762 | 99.0164 | 72.2070 | 1561 | 52 | 1510 | 15 | 11 | 73.3333 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.1370 | 98.6663 | 99.6121 | 66.8126 | 3847 | 52 | 3852 | 15 | 10 | 66.6667 | |
| jlack-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.9413 | 99.8121 | 98.0856 | 65.0500 | 27626 | 52 | 27616 | 539 | 26 | 4.8238 | |
| jli-custom | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.3529 | 98.9842 | 99.7244 | 73.0843 | 5067 | 52 | 5065 | 14 | 7 | 50.0000 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | het | 95.9472 | 94.6281 | 97.3036 | 80.6048 | 916 | 52 | 830 | 23 | 15 | 65.2174 | |
| ckim-isaac | INDEL | D6_15 | map_l150_m2_e0 | * | 53.0973 | 36.5854 | 96.7742 | 93.8247 | 30 | 52 | 30 | 1 | 1 | 100.0000 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 72.3074 | 65.1007 | 81.3084 | 71.2366 | 97 | 52 | 87 | 20 | 14 | 70.0000 | |
| ckim-isaac | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 96.8542 | 94.3107 | 99.5386 | 63.3094 | 862 | 52 | 863 | 4 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.4939 | 96.6013 | 98.4032 | 85.1394 | 1478 | 52 | 1479 | 24 | 16 | 66.6667 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.4939 | 96.6013 | 98.4032 | 85.1394 | 1478 | 52 | 1479 | 24 | 16 | 66.6667 | |
| dgrover-gatk | SNP | tv | map_l150_m0_e0 | * | 98.5887 | 98.7542 | 98.4237 | 82.7837 | 4122 | 52 | 4121 | 66 | 10 | 15.1515 | |
| egarrison-hhga | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 90.2590 | 88.0734 | 92.5558 | 81.8305 | 384 | 52 | 373 | 30 | 15 | 50.0000 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.0614 | 92.4309 | 97.8462 | 82.1967 | 635 | 52 | 636 | 14 | 12 | 85.7143 | |
| egarrison-hhga | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.7960 | 99.6973 | 99.8950 | 55.4424 | 17125 | 52 | 17126 | 18 | 14 | 77.7778 | |
| egarrison-hhga | SNP | * | map_l125_m1_e0 | homalt | 99.8075 | 99.6924 | 99.9229 | 66.3441 | 16853 | 52 | 16853 | 13 | 13 | 100.0000 | |
| egarrison-hhga | SNP | * | map_l125_m2_e0 | homalt | 99.8127 | 99.7007 | 99.9250 | 68.9614 | 17323 | 52 | 17323 | 13 | 13 | 100.0000 | |
| egarrison-hhga | SNP | * | map_l125_m2_e1 | homalt | 99.8144 | 99.7034 | 99.9257 | 69.0000 | 17480 | 52 | 17480 | 13 | 13 | 100.0000 | |
| eyeh-varpipe | INDEL | * | map_l150_m1_e0 | * | 96.5735 | 96.1136 | 97.0378 | 95.4187 | 1286 | 52 | 1769 | 54 | 37 | 68.5185 | |
| ckim-vqsr | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.6992 | 99.3022 | 98.1034 | 41.3093 | 7400 | 52 | 7397 | 143 | 1 | 0.6993 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.9101 | 98.0611 | 99.7739 | 42.7400 | 2630 | 52 | 2648 | 6 | 6 | 100.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 93.6119 | 88.1549 | 99.7890 | 35.1573 | 387 | 52 | 473 | 1 | 1 | 100.0000 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 84.0471 | 96.0902 | 74.6866 | 62.8554 | 1278 | 52 | 2800 | 949 | 275 | 28.9779 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 81.9826 | 70.2857 | 98.3498 | 45.7961 | 123 | 52 | 298 | 5 | 4 | 80.0000 | |
| qzeng-custom | SNP | ti | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5290 | 99.4853 | 99.5728 | 52.8503 | 10050 | 52 | 10023 | 43 | 23 | 53.4884 | |
| qzeng-custom | SNP | tv | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.6831 | 99.5234 | 99.8433 | 60.8736 | 10859 | 52 | 10830 | 17 | 7 | 41.1765 | |
| ltrigg-rtg2 | SNP | ti | map_l125_m1_e0 | homalt | 99.7369 | 99.5292 | 99.9454 | 62.9489 | 10993 | 52 | 10993 | 6 | 6 | 100.0000 | |
| ltrigg-rtg2 | SNP | ti | map_l125_m2_e0 | homalt | 99.7442 | 99.5422 | 99.9470 | 65.7720 | 11306 | 52 | 11306 | 6 | 6 | 100.0000 | |
| ltrigg-rtg2 | SNP | ti | map_l125_m2_e1 | homalt | 99.7464 | 99.5462 | 99.9474 | 65.8140 | 11406 | 52 | 11407 | 6 | 6 | 100.0000 | |