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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
62201-62250 / 86044 show all | |||||||||||||||
| ckim-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.1602 | 97.5584 | 98.7696 | 74.5081 | 919 | 23 | 883 | 11 | 5 | 45.4545 | |
| ckim-gatk | SNP | * | HG002compoundhet | homalt | 99.4644 | 99.0354 | 99.8971 | 35.0629 | 10678 | 104 | 10677 | 11 | 10 | 90.9091 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.8455 | 99.9742 | 99.7171 | 60.4476 | 3877 | 1 | 3877 | 11 | 0 | 0.0000 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.7800 | 100.0000 | 99.5609 | 62.1372 | 2494 | 0 | 2494 | 11 | 0 | 0.0000 | |
| ckim-gatk | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.4505 | 99.3666 | 99.5347 | 87.4509 | 2353 | 15 | 2353 | 11 | 10 | 90.9091 | |
| ckim-gatk | SNP | * | map_l100_m2_e0 | homalt | 83.9525 | 72.3722 | 99.9448 | 68.4557 | 19919 | 7604 | 19919 | 11 | 7 | 63.6364 | |
| ckim-gatk | SNP | * | map_l100_m2_e1 | homalt | 84.0675 | 72.5428 | 99.9455 | 68.3772 | 20164 | 7632 | 20164 | 11 | 7 | 63.6364 | |
| ckim-gatk | SNP | tv | HG002complexvar | homalt | 99.2138 | 98.4513 | 99.9883 | 23.0317 | 93638 | 1473 | 93624 | 11 | 8 | 72.7273 | |
| ckim-gatk | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | het | 99.6925 | 99.7409 | 99.6441 | 69.2652 | 3080 | 8 | 3080 | 11 | 9 | 81.8182 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | hetalt | 79.5118 | 70.0599 | 91.9118 | 65.9148 | 117 | 50 | 125 | 11 | 10 | 90.9091 | |
| ckim-isaac | INDEL | * | map_siren | homalt | 82.0615 | 69.8682 | 99.4105 | 72.7551 | 1855 | 800 | 1855 | 11 | 7 | 63.6364 | |
| ciseli-custom | SNP | tv | lowcmp_SimpleRepeat_triTR_51to200 | het | 15.3846 | 100.0000 | 8.3333 | 80.6452 | 1 | 0 | 1 | 11 | 0 | 0.0000 | |
| ckim-dragen | INDEL | * | func_cds | het | 97.2603 | 99.5327 | 95.0893 | 57.2519 | 213 | 1 | 213 | 11 | 0 | 0.0000 | |
| ckim-dragen | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.6285 | 99.8409 | 99.4171 | 72.8645 | 1883 | 3 | 1876 | 11 | 8 | 72.7273 | |
| ckim-dragen | INDEL | * | map_l125_m2_e0 | homalt | 98.4233 | 98.2962 | 98.5507 | 86.5115 | 750 | 13 | 748 | 11 | 6 | 54.5455 | |
| ckim-dragen | INDEL | * | map_l125_m2_e1 | homalt | 98.4458 | 98.3204 | 98.5714 | 86.6180 | 761 | 13 | 759 | 11 | 6 | 54.5455 | |
| ckim-dragen | INDEL | * | map_l250_m0_e0 | * | 92.1212 | 97.4359 | 87.3563 | 97.7177 | 76 | 2 | 76 | 11 | 1 | 9.0909 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.0937 | 99.5146 | 98.6763 | 71.9257 | 820 | 4 | 820 | 11 | 1 | 9.0909 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 36.9771 | 25.1969 | 69.4444 | 73.3333 | 32 | 95 | 25 | 11 | 0 | 0.0000 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | hetalt | 50.2732 | 40.0000 | 67.6471 | 91.9622 | 24 | 36 | 23 | 11 | 2 | 18.1818 | |
| gduggal-snapplat | INDEL | I1_5 | map_l150_m2_e0 | homalt | 86.3737 | 80.0995 | 93.7143 | 93.0223 | 161 | 40 | 164 | 11 | 0 | 0.0000 | |
| gduggal-snapplat | INDEL | I1_5 | map_l150_m2_e1 | homalt | 86.2888 | 79.9020 | 93.7853 | 93.0913 | 163 | 41 | 166 | 11 | 0 | 0.0000 | |
| gduggal-snapplat | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 0.0000 | 0.0000 | 79.2453 | 0 | 35 | 0 | 11 | 0 | 0.0000 | ||
| gduggal-snapplat | INDEL | I6_15 | map_l100_m1_e0 | * | 17.3913 | 10.5263 | 50.0000 | 94.3445 | 12 | 102 | 11 | 11 | 0 | 0.0000 | |
| gduggal-snapplat | INDEL | I6_15 | map_l100_m2_e0 | * | 17.1429 | 10.3448 | 50.0000 | 94.9192 | 12 | 104 | 11 | 11 | 0 | 0.0000 | |
| gduggal-snapplat | INDEL | I6_15 | map_l100_m2_e1 | * | 17.1429 | 10.3448 | 50.0000 | 95.0339 | 12 | 104 | 11 | 11 | 0 | 0.0000 | |
| gduggal-snapplat | SNP | * | map_l100_m0_e0 | homalt | 93.3571 | 87.6248 | 99.8920 | 65.0376 | 10182 | 1438 | 10176 | 11 | 11 | 100.0000 | |
| gduggal-snapvard | SNP | tv | map_l125_m1_e0 | homalt | 98.0991 | 96.4505 | 99.8050 | 66.5043 | 5652 | 208 | 5629 | 11 | 8 | 72.7273 | |
| ghariani-varprowl | INDEL | * | map_l150_m2_e1 | homalt | 94.6597 | 91.8699 | 97.6242 | 87.5504 | 452 | 40 | 452 | 11 | 4 | 36.3636 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 44.9438 | 31.4961 | 78.4314 | 66.6667 | 40 | 87 | 40 | 11 | 11 | 100.0000 | |
| ghariani-varprowl | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_gt10 | het | 77.0340 | 78.5714 | 75.5556 | 99.4804 | 33 | 9 | 34 | 11 | 6 | 54.5455 | |
| gduggal-snapfb | SNP | * | map_l250_m0_e0 | homalt | 95.3393 | 92.6868 | 98.1481 | 96.7438 | 583 | 46 | 583 | 11 | 5 | 45.4545 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 17.3710 | 9.5750 | 93.4911 | 35.2490 | 187 | 1766 | 158 | 11 | 11 | 100.0000 | |
| gduggal-snapvard | INDEL | I6_15 | map_l150_m0_e0 | * | 61.5942 | 62.5000 | 60.7143 | 91.7889 | 5 | 3 | 17 | 11 | 8 | 72.7273 | |
| gduggal-snapvard | INDEL | I6_15 | map_l150_m0_e0 | het | 74.4186 | 100.0000 | 59.2593 | 91.4013 | 4 | 0 | 16 | 11 | 8 | 72.7273 | |
| gduggal-snapvard | SNP | * | tech_badpromoters | * | 88.3476 | 84.7134 | 92.3077 | 52.4917 | 133 | 24 | 132 | 11 | 2 | 18.1818 | |
| gduggal-snapvard | SNP | * | tech_badpromoters | het | 86.4516 | 87.0130 | 85.8974 | 57.3770 | 67 | 10 | 67 | 11 | 2 | 18.1818 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 92.1833 | 90.4762 | 93.9560 | 39.3333 | 418 | 44 | 171 | 11 | 10 | 90.9091 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | homalt | 70.2703 | 100.0000 | 54.1667 | 50.0000 | 13 | 0 | 13 | 11 | 7 | 63.6364 | |
| gduggal-snapfb | INDEL | D1_5 | map_l250_m1_e0 | * | 95.1009 | 96.4912 | 93.7500 | 94.8882 | 165 | 6 | 165 | 11 | 1 | 9.0909 | |
| gduggal-snapfb | INDEL | D1_5 | map_l250_m1_e0 | het | 93.4498 | 96.3964 | 90.6780 | 93.2610 | 107 | 4 | 107 | 11 | 1 | 9.0909 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 73.7705 | 60.1604 | 95.3390 | 57.0128 | 225 | 149 | 225 | 11 | 10 | 90.9091 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | hetalt | 42.8116 | 28.1132 | 89.7196 | 42.4731 | 149 | 381 | 96 | 11 | 10 | 90.9091 | |
| ghariani-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 48.6558 | 37.7049 | 68.5714 | 84.9138 | 23 | 38 | 24 | 11 | 10 | 90.9091 | |
| ghariani-varprowl | INDEL | I1_5 | func_cds | * | 94.1828 | 94.4444 | 93.9227 | 43.4375 | 170 | 10 | 170 | 11 | 7 | 63.6364 | |
| ghariani-varprowl | INDEL | I1_5 | map_l100_m2_e1 | homalt | 97.0093 | 96.1111 | 97.9245 | 77.2337 | 519 | 21 | 519 | 11 | 6 | 54.5455 | |
| ghariani-varprowl | INDEL | I1_5 | map_l250_m1_e0 | het | 90.7692 | 98.3333 | 84.2857 | 97.7827 | 59 | 1 | 59 | 11 | 3 | 27.2727 | |
| ghariani-varprowl | INDEL | I6_15 | map_l125_m1_e0 | * | 70.7071 | 66.0377 | 76.0870 | 91.4019 | 35 | 18 | 35 | 11 | 7 | 63.6364 | |
| ghariani-varprowl | INDEL | I6_15 | map_l125_m2_e0 | * | 70.7071 | 66.0377 | 76.0870 | 92.4959 | 35 | 18 | 35 | 11 | 7 | 63.6364 | |
| ghariani-varprowl | INDEL | I6_15 | map_l125_m2_e1 | * | 70.7071 | 66.0377 | 76.0870 | 92.6518 | 35 | 18 | 35 | 11 | 7 | 63.6364 | |