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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
54701-54750 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | I6_15 | * | homalt | 97.7408 | 99.8557 | 95.7136 | 54.8957 | 6230 | 9 | 6230 | 279 | 277 | 99.2832 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.6885 | 99.4406 | 99.9375 | 43.4875 | 1600 | 9 | 1600 | 1 | 1 | 100.0000 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.3727 | 99.4055 | 99.3399 | 88.6347 | 1505 | 9 | 1505 | 10 | 9 | 90.0000 | |
| ckim-vqsr | SNP | * | map_l125_m0_e0 | hetalt | 0.0000 | 100.0000 | 0 | 9 | 0 | 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_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 99.0685 | 99.0142 | 99.1228 | 89.4371 | 904 | 9 | 904 | 8 | 7 | 87.5000 | |
| ckim-vqsr | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.7164 | 99.4907 | 99.9431 | 60.9458 | 1758 | 9 | 1758 | 1 | 1 | 100.0000 | |
| ckim-vqsr | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.6556 | 99.3135 | 100.0000 | 34.6057 | 1302 | 9 | 1302 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | map_l125_m0_e0 | hetalt | 0.0000 | 100.0000 | 0 | 9 | 0 | 0 | 0 | ||||
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 95.0745 | 98.9726 | 91.4718 | 82.4269 | 867 | 9 | 665 | 62 | 60 | 96.7742 | |
| dgrover-gatk | INDEL | D16_PLUS | map_l100_m2_e1 | * | 87.1287 | 90.7216 | 83.8095 | 94.9324 | 88 | 9 | 88 | 17 | 4 | 23.5294 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m0_e0 | het | 97.9819 | 98.4772 | 97.4916 | 87.0169 | 582 | 9 | 583 | 15 | 2 | 13.3333 | |
| dgrover-gatk | INDEL | D1_5 | map_l125_m0_e0 | * | 97.7938 | 98.1855 | 97.4052 | 89.6850 | 487 | 9 | 488 | 13 | 3 | 23.0769 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 87.5304 | 79.5455 | 97.2973 | 66.0550 | 35 | 9 | 36 | 1 | 0 | 0.0000 | |
| ckim-isaac | SNP | * | map_l100_m0_e0 | hetalt | 60.8696 | 43.7500 | 100.0000 | 79.4118 | 7 | 9 | 7 | 0 | 0 | ||
| ckim-isaac | SNP | ti | map_l150_m1_e0 | hetalt | 57.1429 | 40.0000 | 100.0000 | 83.7838 | 6 | 9 | 6 | 0 | 0 | ||
| ckim-isaac | SNP | ti | map_l150_m2_e0 | hetalt | 57.1429 | 40.0000 | 100.0000 | 85.3659 | 6 | 9 | 6 | 0 | 0 | ||
| ckim-isaac | SNP | ti | map_l150_m2_e1 | hetalt | 57.1429 | 40.0000 | 100.0000 | 85.7143 | 6 | 9 | 6 | 0 | 0 | ||
| ckim-isaac | SNP | ti | tech_badpromoters | het | 88.6076 | 79.5455 | 100.0000 | 43.5484 | 35 | 9 | 35 | 0 | 0 | ||
| ckim-isaac | SNP | tv | map_l100_m0_e0 | hetalt | 60.8696 | 43.7500 | 100.0000 | 79.4118 | 7 | 9 | 7 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 96.3583 | 95.9459 | 96.7742 | 64.4262 | 213 | 9 | 210 | 7 | 4 | 57.1429 | |
| ckim-isaac | INDEL | I6_15 | map_l100_m0_e0 | het | 58.3333 | 41.1765 | 100.0000 | 96.3636 | 7 | 10 | 6 | 0 | 0 | ||
| ckim-isaac | INDEL | I6_15 | map_l100_m0_e0 | homalt | 28.5714 | 16.6667 | 100.0000 | 91.6667 | 2 | 10 | 2 | 0 | 0 | ||
| ckim-isaac | INDEL | I6_15 | map_l100_m1_e0 | hetalt | 70.5882 | 54.5455 | 100.0000 | 82.1918 | 12 | 10 | 13 | 0 | 0 | ||
| ckim-isaac | INDEL | I6_15 | map_l100_m2_e0 | hetalt | 70.5882 | 54.5455 | 100.0000 | 84.1463 | 12 | 10 | 13 | 0 | 0 | ||
| ckim-isaac | INDEL | I6_15 | map_l100_m2_e1 | hetalt | 70.5882 | 54.5455 | 100.0000 | 84.7059 | 12 | 10 | 13 | 0 | 0 | ||
| ckim-isaac | INDEL | I6_15 | map_l125_m0_e0 | * | 50.0000 | 33.3333 | 100.0000 | 96.7949 | 5 | 10 | 5 | 0 | 0 | ||
| ckim-isaac | INDEL | I6_15 | segdup | homalt | 88.0952 | 78.7234 | 100.0000 | 87.9870 | 37 | 10 | 37 | 0 | 0 | ||
| 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 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 95.2384 | 92.4812 | 98.1651 | 88.0482 | 123 | 10 | 107 | 2 | 2 | 100.0000 | |
| dgrover-gatk | INDEL | I1_5 | HG002complexvar | homalt | 99.8663 | 99.9256 | 99.8070 | 53.0009 | 13438 | 10 | 13443 | 26 | 25 | 96.1538 | |
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 93.6709 | 88.0952 | 100.0000 | 59.7826 | 74 | 10 | 74 | 0 | 0 | ||
| dgrover-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.3559 | 99.2492 | 99.4628 | 72.8768 | 1322 | 10 | 1296 | 7 | 5 | 71.4286 | |
| dgrover-gatk | INDEL | I1_5 | map_l125_m1_e0 | het | 98.3497 | 97.9424 | 98.7603 | 87.9181 | 476 | 10 | 478 | 6 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l125_m2_e0 | het | 98.3863 | 97.9879 | 98.7879 | 88.9681 | 487 | 10 | 489 | 6 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l125_m2_e1 | het | 98.4213 | 98.0315 | 98.8142 | 89.0239 | 498 | 10 | 500 | 6 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 97.0618 | 95.9514 | 98.1982 | 81.3445 | 237 | 10 | 218 | 4 | 2 | 50.0000 | |
| dgrover-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_51to200 | * | 95.0000 | 93.0070 | 97.0803 | 92.7552 | 133 | 10 | 133 | 4 | 3 | 75.0000 | |
| dgrover-gatk | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 99.5490 | 99.1830 | 99.9177 | 59.2008 | 1214 | 10 | 1214 | 1 | 1 | 100.0000 | |
| dgrover-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 99.3818 | 99.2284 | 99.5356 | 87.4927 | 1286 | 10 | 1286 | 6 | 6 | 100.0000 | |
| dgrover-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.7720 | 99.5863 | 99.9585 | 73.0075 | 2407 | 10 | 2407 | 1 | 1 | 100.0000 | |
| dgrover-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | * | 99.8552 | 99.7933 | 99.9172 | 69.3872 | 4827 | 10 | 4827 | 4 | 3 | 75.0000 | |
| dgrover-gatk | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.3508 | 99.8517 | 98.8550 | 44.7482 | 6734 | 10 | 6734 | 78 | 1 | 1.2821 | |
| dgrover-gatk | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 99.3666 | 99.2968 | 99.4366 | 88.7015 | 1412 | 10 | 1412 | 8 | 7 | 87.5000 | |
| egarrison-hhga | INDEL | * | map_l100_m0_e0 | hetalt | 80.4899 | 69.6970 | 95.2381 | 93.4375 | 23 | 10 | 20 | 1 | 0 | 0.0000 | |
| egarrison-hhga | INDEL | * | map_l125_m2_e0 | homalt | 98.8838 | 98.6894 | 99.0789 | 86.4407 | 753 | 10 | 753 | 7 | 4 | 57.1429 | |
| egarrison-hhga | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 95.5603 | 97.8355 | 93.3884 | 59.3960 | 452 | 10 | 452 | 32 | 19 | 59.3750 | |
| egarrison-hhga | INDEL | D1_5 | HG002compoundhet | homalt | 76.1097 | 96.5636 | 62.8062 | 73.3847 | 281 | 10 | 282 | 167 | 153 | 91.6168 | |