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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
60901-60950 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | * | map_l150_m2_e1 | het | 94.7936 | 94.4805 | 95.1087 | 94.5035 | 873 | 51 | 875 | 45 | 4 | 8.8889 | |
| ckim-vqsr | INDEL | D16_PLUS | HG002complexvar | homalt | 98.7952 | 99.3080 | 98.2877 | 76.3371 | 287 | 2 | 287 | 5 | 4 | 80.0000 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.4553 | 99.3353 | 99.5755 | 60.7194 | 1644 | 11 | 1642 | 7 | 4 | 57.1429 | |
| dgrover-gatk | INDEL | D6_15 | segdup | * | 96.3351 | 96.3351 | 96.3351 | 93.8821 | 184 | 7 | 184 | 7 | 4 | 57.1429 | |
| dgrover-gatk | INDEL | D6_15 | segdup | homalt | 96.1538 | 100.0000 | 92.5926 | 92.4051 | 50 | 0 | 50 | 4 | 4 | 100.0000 | |
| dgrover-gatk | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.6602 | 96.7890 | 98.5472 | 85.8707 | 422 | 14 | 407 | 6 | 4 | 66.6667 | |
| dgrover-gatk | INDEL | I1_5 | * | hetalt | 97.2805 | 94.7387 | 99.9625 | 62.4322 | 10606 | 589 | 10669 | 4 | 4 | 100.0000 | |
| dgrover-gatk | INDEL | I1_5 | HG002complexvar | hetalt | 98.0896 | 96.4658 | 99.7691 | 70.7729 | 1665 | 61 | 1728 | 4 | 4 | 100.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l100_m1_e0 | * | 98.9542 | 98.8051 | 99.1038 | 84.0367 | 1323 | 16 | 1327 | 12 | 4 | 33.3333 | |
| dgrover-gatk | INDEL | I1_5 | map_l100_m1_e0 | homalt | 99.4231 | 99.8069 | 99.0421 | 80.9489 | 517 | 1 | 517 | 5 | 4 | 80.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l100_m2_e0 | * | 98.9764 | 98.8304 | 99.1228 | 85.1466 | 1352 | 16 | 1356 | 12 | 4 | 33.3333 | |
| dgrover-gatk | INDEL | I1_5 | map_l100_m2_e0 | homalt | 99.4371 | 99.8117 | 99.0654 | 82.2730 | 530 | 1 | 530 | 5 | 4 | 80.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_l100_m2_e1 | * | 98.9962 | 98.8530 | 99.1398 | 85.2131 | 1379 | 16 | 1383 | 12 | 4 | 33.3333 | |
| dgrover-gatk | INDEL | I1_5 | map_l100_m2_e1 | homalt | 99.4465 | 99.8148 | 99.0809 | 82.3434 | 539 | 1 | 539 | 5 | 4 | 80.0000 | |
| dgrover-gatk | INDEL | I1_5 | map_siren | homalt | 99.6298 | 99.7525 | 99.5074 | 78.6951 | 1209 | 3 | 1212 | 6 | 4 | 66.6667 | |
| dgrover-gatk | INDEL | I6_15 | * | hetalt | 96.6039 | 93.4744 | 99.9502 | 38.7907 | 7993 | 558 | 8034 | 4 | 4 | 100.0000 | |
| dgrover-gatk | INDEL | I6_15 | HG002complexvar | het | 99.4230 | 99.0658 | 99.7827 | 59.6952 | 2333 | 22 | 2296 | 5 | 4 | 80.0000 | |
| dgrover-gatk | INDEL | I6_15 | map_siren | * | 97.1901 | 96.3934 | 98.0000 | 85.1852 | 294 | 11 | 294 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 97.7836 | 97.1503 | 98.4252 | 91.2111 | 375 | 11 | 375 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 97.6407 | 97.4638 | 97.8182 | 91.2809 | 269 | 7 | 269 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.9143 | 99.8827 | 99.9458 | 56.3849 | 11071 | 13 | 11067 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.9343 | 99.9343 | 99.9343 | 54.4380 | 6084 | 4 | 6084 | 4 | 4 | 100.0000 | |
| dgrover-gatk | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3002 | 99.9010 | 98.7065 | 40.6968 | 18165 | 18 | 18162 | 238 | 4 | 1.6807 | |
| dgrover-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.5922 | 99.5471 | 99.6374 | 86.6820 | 1099 | 5 | 1099 | 4 | 4 | 100.0000 | |
| dgrover-gatk | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 99.5839 | 99.7222 | 99.4460 | 87.8981 | 718 | 2 | 718 | 4 | 4 | 100.0000 | |
| dgrover-gatk | SNP | ti | map_l150_m0_e0 | homalt | 99.3450 | 98.8772 | 99.8172 | 73.4053 | 2730 | 31 | 2730 | 5 | 4 | 80.0000 | |
| dgrover-gatk | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.9009 | 99.8415 | 99.9603 | 61.7282 | 10081 | 16 | 10081 | 4 | 4 | 100.0000 | |
| dgrover-gatk | SNP | tv | map_l150_m1_e0 | homalt | 99.4146 | 98.9863 | 99.8466 | 69.3080 | 3906 | 40 | 3906 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | tv | map_l150_m2_e0 | homalt | 99.4343 | 99.0203 | 99.8518 | 71.6158 | 4043 | 40 | 4043 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | tv | map_l150_m2_e1 | homalt | 99.4413 | 99.0324 | 99.8537 | 71.5870 | 4094 | 40 | 4094 | 6 | 4 | 66.6667 | |
| dgrover-gatk | SNP | tv | map_l250_m0_e0 | * | 96.9974 | 97.1242 | 96.8709 | 93.8566 | 743 | 22 | 743 | 24 | 4 | 16.6667 | |
| egarrison-hhga | INDEL | * | map_l100_m0_e0 | homalt | 98.5251 | 98.4283 | 98.6220 | 83.5599 | 501 | 8 | 501 | 7 | 4 | 57.1429 | |
| egarrison-hhga | INDEL | * | map_l125_m0_e0 | het | 97.1036 | 96.9336 | 97.2743 | 89.2313 | 569 | 18 | 571 | 16 | 4 | 25.0000 | |
| egarrison-hhga | INDEL | * | map_l125_m1_e0 | homalt | 98.9056 | 98.7705 | 99.0411 | 85.3443 | 723 | 9 | 723 | 7 | 4 | 57.1429 | |
| 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 | * | map_l125_m2_e1 | homalt | 98.8342 | 98.5788 | 99.0909 | 86.5970 | 763 | 11 | 763 | 7 | 4 | 57.1429 | |
| egarrison-hhga | INDEL | * | map_l150_m0_e0 | het | 95.7536 | 95.6012 | 95.9064 | 92.1703 | 326 | 15 | 328 | 14 | 4 | 28.5714 | |
| egarrison-hhga | INDEL | * | map_l150_m1_e0 | homalt | 98.3749 | 98.2684 | 98.4816 | 88.2067 | 454 | 8 | 454 | 7 | 4 | 57.1429 | |
| egarrison-hhga | INDEL | * | map_l150_m2_e0 | homalt | 98.4391 | 98.3368 | 98.5417 | 89.3000 | 473 | 8 | 473 | 7 | 4 | 57.1429 | |
| egarrison-hhga | INDEL | * | map_l150_m2_e1 | homalt | 98.4741 | 98.3740 | 98.5743 | 89.3400 | 484 | 8 | 484 | 7 | 4 | 57.1429 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 89.4737 | 82.0175 | 98.4211 | 51.7154 | 748 | 164 | 748 | 12 | 4 | 33.3333 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 82.5264 | 78.6070 | 86.8571 | 81.0401 | 158 | 43 | 152 | 23 | 4 | 17.3913 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 63.1579 | 54.5455 | 75.0000 | 88.2353 | 6 | 5 | 12 | 4 | 4 | 100.0000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 89.9729 | 83.2080 | 97.9351 | 51.7094 | 332 | 67 | 332 | 7 | 4 | 57.1429 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 82.4914 | 70.8428 | 98.7245 | 40.6959 | 311 | 128 | 387 | 5 | 4 | 80.0000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 89.9500 | 88.4615 | 91.4894 | 71.1656 | 46 | 6 | 43 | 4 | 4 | 100.0000 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 76.7173 | 62.8571 | 98.4190 | 46.7368 | 220 | 130 | 249 | 4 | 4 | 100.0000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 81.5419 | 72.4638 | 93.2203 | 60.1351 | 50 | 19 | 55 | 4 | 4 | 100.0000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 83.9902 | 73.3509 | 98.2394 | 46.3138 | 278 | 101 | 279 | 5 | 4 | 80.0000 | |
| ckim-isaac | INDEL | D1_5 | map_l100_m0_e0 | * | 80.7640 | 68.5979 | 98.1758 | 85.4699 | 592 | 271 | 592 | 11 | 4 | 36.3636 | |