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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
61901-61950 / 86044 show all | |||||||||||||||
| ckim-vqsr | SNP | tv | * | hetalt | 97.4148 | 95.1780 | 99.7593 | 54.6645 | 829 | 42 | 829 | 2 | 2 | 100.0000 | |
| ckim-vqsr | SNP | tv | * | homalt | 98.8369 | 97.7055 | 99.9948 | 20.5893 | 368470 | 8653 | 368456 | 19 | 16 | 84.2105 | |
| ckim-vqsr | SNP | tv | HG002complexvar | * | 98.6339 | 97.3216 | 99.9820 | 22.8566 | 239559 | 6593 | 239468 | 43 | 20 | 46.5116 | |
| ckim-vqsr | SNP | tv | HG002complexvar | het | 98.9859 | 98.0150 | 99.9763 | 22.4456 | 147739 | 2992 | 147662 | 35 | 14 | 40.0000 | |
| ckim-vqsr | SNP | tv | HG002complexvar | hetalt | 96.6667 | 93.5484 | 100.0000 | 40.6953 | 290 | 20 | 290 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | HG002complexvar | homalt | 98.0771 | 96.2349 | 99.9913 | 23.4384 | 91530 | 3581 | 91516 | 8 | 6 | 75.0000 | |
| ckim-vqsr | SNP | tv | HG002compoundhet | * | 98.8066 | 97.8931 | 99.7373 | 49.7301 | 8735 | 188 | 8732 | 23 | 15 | 65.2174 | |
| ckim-vqsr | SNP | tv | HG002compoundhet | het | 99.1184 | 98.6518 | 99.5894 | 55.9836 | 4610 | 63 | 4608 | 19 | 12 | 63.1579 | |
| ckim-vqsr | SNP | tv | HG002compoundhet | hetalt | 97.5030 | 95.1276 | 100.0000 | 23.3645 | 820 | 42 | 820 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | HG002compoundhet | homalt | 98.7009 | 97.5502 | 99.8791 | 43.2979 | 3305 | 83 | 3304 | 4 | 3 | 75.0000 | |
| ckim-vqsr | SNP | tv | decoy | * | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| ckim-vqsr | SNP | tv | decoy | het | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| ckim-vqsr | SNP | tv | decoy | hetalt | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| ckim-vqsr | SNP | tv | decoy | homalt | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| ckim-vqsr | SNP | tv | func_cds | * | 99.7367 | 99.6568 | 99.8166 | 38.6616 | 4356 | 15 | 4355 | 8 | 0 | 0.0000 | |
| ckim-vqsr | SNP | tv | func_cds | het | 99.7366 | 99.7742 | 99.6990 | 44.6481 | 2651 | 6 | 2650 | 8 | 0 | 0.0000 | |
| ckim-vqsr | SNP | tv | func_cds | hetalt | 100.0000 | 100.0000 | 100.0000 | 61.5385 | 10 | 0 | 10 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | func_cds | homalt | 99.7352 | 99.4718 | 100.0000 | 25.8206 | 1695 | 9 | 1695 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 99.1719 | 98.7467 | 99.6008 | 69.5995 | 1497 | 19 | 1497 | 6 | 2 | 33.3333 | |
| ckim-vqsr | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 98.8343 | 98.2863 | 99.3884 | 71.8022 | 975 | 17 | 975 | 6 | 2 | 33.3333 | |
| ckim-vqsr | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| ckim-vqsr | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 99.8088 | 99.6183 | 100.0000 | 64.2221 | 522 | 2 | 522 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | lowcmp_AllRepeats_gt200bp_gt95identity_merged | * | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| ckim-vqsr | SNP | tv | lowcmp_AllRepeats_gt200bp_gt95identity_merged | het | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| ckim-vqsr | SNP | tv | lowcmp_AllRepeats_gt200bp_gt95identity_merged | hetalt | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| ckim-vqsr | SNP | tv | lowcmp_AllRepeats_gt200bp_gt95identity_merged | homalt | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| ckim-vqsr | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.3676 | 99.3641 | 99.3711 | 65.4796 | 27502 | 176 | 27492 | 174 | 18 | 10.3448 | |
| ckim-vqsr | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2929 | 99.5560 | 99.0312 | 67.2462 | 17490 | 78 | 17480 | 171 | 15 | 8.7719 | |
| ckim-vqsr | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.0000 | 92.3077 | 100.0000 | 83.3333 | 12 | 1 | 12 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5025 | 99.0393 | 99.9700 | 61.7944 | 10000 | 97 | 10000 | 3 | 3 | 100.0000 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9598 | 98.5931 | 99.3293 | 80.6409 | 14366 | 205 | 14366 | 97 | 14 | 14.4330 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.8377 | 98.6970 | 98.9788 | 83.4427 | 9014 | 119 | 9014 | 93 | 10 | 10.7527 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 100.0000 | 100.0000 | 100.0000 | 94.2529 | 15 | 0 | 15 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.1639 | 98.4142 | 99.9251 | 72.5328 | 5337 | 86 | 5337 | 4 | 4 | 100.0000 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 99.4741 | 99.1018 | 99.8492 | 51.2858 | 1324 | 12 | 1324 | 2 | 0 | 0.0000 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 99.2357 | 98.7135 | 99.7636 | 54.0717 | 844 | 11 | 844 | 2 | 0 | 0.0000 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.8959 | 99.7921 | 100.0000 | 45.3303 | 480 | 1 | 480 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_gt200bp_gt95identity_merged | * | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_gt200bp_gt95identity_merged | het | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| ckim-vqsr | INDEL | I1_5 | map_l150_m2_e0 | hetalt | 100.0000 | 100.0000 | 100.0000 | 95.8140 | 9 | 0 | 9 | 0 | 0 | ||
| ckim-vqsr | INDEL | I1_5 | map_l150_m2_e0 | homalt | 99.2556 | 99.5025 | 99.0099 | 88.8950 | 200 | 1 | 200 | 2 | 1 | 50.0000 | |
| ckim-vqsr | INDEL | I1_5 | map_l150_m2_e1 | * | 96.5736 | 95.4802 | 97.6923 | 93.3153 | 507 | 24 | 508 | 12 | 2 | 16.6667 | |
| ckim-vqsr | INDEL | I1_5 | map_l150_m2_e1 | het | 94.6912 | 92.7445 | 96.7213 | 94.6529 | 294 | 23 | 295 | 10 | 1 | 10.0000 | |
| ckim-vqsr | INDEL | I1_5 | map_l150_m2_e1 | hetalt | 100.0000 | 100.0000 | 100.0000 | 95.4545 | 10 | 0 | 10 | 0 | 0 | ||
| ckim-vqsr | INDEL | I1_5 | map_l150_m2_e1 | homalt | 99.2665 | 99.5098 | 99.0244 | 88.9488 | 203 | 1 | 203 | 2 | 1 | 50.0000 | |
| ckim-vqsr | INDEL | I1_5 | map_l250_m0_e0 | * | 86.2745 | 91.6667 | 81.4815 | 98.6855 | 22 | 2 | 22 | 5 | 1 | 20.0000 | |
| ckim-vqsr | INDEL | I1_5 | map_l250_m0_e0 | het | 81.2500 | 86.6667 | 76.4706 | 98.9875 | 13 | 2 | 13 | 4 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | I1_5 | map_l250_m0_e0 | hetalt | 0.0000 | 100.0000 | 0 | 0 | 0 | 0 | 0 | ||||
| ckim-vqsr | INDEL | I1_5 | map_l250_m0_e0 | homalt | 94.7368 | 100.0000 | 90.0000 | 96.9880 | 9 | 0 | 9 | 1 | 1 | 100.0000 | |