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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
43151-43200 / 86044 show all | |||||||||||||||
| ckim-vqsr | INDEL | * | HG002compoundhet | homalt | 61.0714 | 99.7085 | 44.0154 | 84.7468 | 684 | 2 | 684 | 870 | 867 | 99.6552 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7617 | 99.8940 | 99.6298 | 72.7247 | 1884 | 2 | 1884 | 7 | 5 | 71.4286 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.9064 | 99.9065 | 99.9064 | 76.8906 | 2136 | 2 | 2134 | 2 | 1 | 50.0000 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.6908 | 99.5935 | 97.8044 | 62.6398 | 490 | 2 | 490 | 11 | 9 | 81.8182 | |
| ckim-vqsr | INDEL | * | map_l125_m0_e0 | homalt | 98.9474 | 99.2958 | 98.6014 | 88.7224 | 282 | 2 | 282 | 4 | 3 | 75.0000 | |
| ckim-vqsr | INDEL | * | map_l250_m0_e0 | het | 83.6066 | 96.2264 | 73.9130 | 98.5907 | 51 | 2 | 51 | 18 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | * | map_l250_m1_e0 | hetalt | 80.0000 | 66.6667 | 100.0000 | 98.1308 | 4 | 2 | 4 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | map_l250_m1_e0 | homalt | 98.6175 | 98.1651 | 99.0741 | 95.2880 | 107 | 2 | 107 | 1 | 1 | 100.0000 | |
| ckim-vqsr | INDEL | * | map_l250_m2_e0 | hetalt | 80.0000 | 66.6667 | 100.0000 | 98.4496 | 4 | 2 | 4 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | map_l250_m2_e0 | homalt | 98.6900 | 98.2609 | 99.1228 | 95.6900 | 113 | 2 | 113 | 1 | 1 | 100.0000 | |
| ckim-vqsr | INDEL | * | map_l250_m2_e1 | hetalt | 80.0000 | 66.6667 | 100.0000 | 98.4791 | 4 | 2 | 4 | 0 | 0 | ||
| ckim-vqsr | INDEL | * | map_l250_m2_e1 | homalt | 98.7013 | 98.2759 | 99.1304 | 95.7549 | 114 | 2 | 114 | 1 | 1 | 100.0000 | |
| ckim-vqsr | INDEL | * | segdup | homalt | 99.3776 | 99.7917 | 98.9669 | 93.6950 | 958 | 2 | 958 | 10 | 9 | 90.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | HG002complexvar | homalt | 98.7952 | 99.3080 | 98.2877 | 76.3371 | 287 | 2 | 287 | 5 | 4 | 80.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 97.8852 | 99.5902 | 96.2376 | 72.0686 | 486 | 2 | 486 | 19 | 18 | 94.7368 | |
| 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_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.8726 | 99.7455 | 100.0000 | 61.9602 | 784 | 2 | 784 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 99.8092 | 99.6190 | 100.0000 | 67.3737 | 523 | 2 | 523 | 0 | 0 | ||
| ckim-vqsr | SNP | tv | lowcmp_SimpleRepeat_quadTR_51to200 | * | 96.3855 | 95.2381 | 97.5610 | 89.5939 | 40 | 2 | 40 | 1 | 0 | 0.0000 | |
| ckim-vqsr | SNP | tv | lowcmp_SimpleRepeat_quadTR_51to200 | het | 95.7746 | 94.4444 | 97.1429 | 88.4488 | 34 | 2 | 34 | 1 | 0 | 0.0000 | |
| ckim-vqsr | SNP | tv | tech_badpromoters | * | 97.9021 | 97.2222 | 98.5915 | 53.2895 | 70 | 2 | 70 | 1 | 1 | 100.0000 | |
| dgrover-gatk | INDEL | * | HG002compoundhet | homalt | 61.4004 | 99.7085 | 44.3580 | 85.1072 | 684 | 2 | 684 | 858 | 856 | 99.7669 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7617 | 99.8940 | 99.6298 | 72.7364 | 1884 | 2 | 1884 | 7 | 5 | 71.4286 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.8597 | 99.9065 | 99.8129 | 76.6441 | 2136 | 2 | 2134 | 4 | 1 | 25.0000 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.7781 | 99.9671 | 99.5898 | 57.9684 | 6070 | 2 | 6070 | 25 | 24 | 96.0000 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.5915 | 99.5935 | 97.6096 | 62.3406 | 490 | 2 | 490 | 12 | 11 | 91.6667 | |
| dgrover-gatk | INDEL | * | map_l100_m0_e0 | hetalt | 95.4305 | 93.9394 | 96.9697 | 91.1051 | 31 | 2 | 32 | 1 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | * | map_l125_m1_e0 | hetalt | 97.4359 | 95.0000 | 100.0000 | 92.6357 | 38 | 2 | 38 | 0 | 0 | ||
| dgrover-gatk | INDEL | * | map_l125_m2_e0 | hetalt | 97.5610 | 95.2381 | 100.0000 | 93.2546 | 40 | 2 | 40 | 0 | 0 | ||
| dgrover-gatk | INDEL | * | map_l150_m2_e1 | hetalt | 95.4545 | 91.3043 | 100.0000 | 95.3846 | 21 | 2 | 21 | 0 | 0 | ||
| dgrover-gatk | INDEL | * | map_l250_m0_e0 | homalt | 92.0000 | 92.0000 | 92.0000 | 97.6482 | 23 | 2 | 23 | 2 | 1 | 50.0000 | |
| dgrover-gatk | INDEL | * | segdup | homalt | 99.4292 | 99.7917 | 99.0693 | 93.7134 | 958 | 2 | 958 | 9 | 8 | 88.8889 | |
| dgrover-gatk | INDEL | D16_PLUS | HG002complexvar | homalt | 98.7952 | 99.3080 | 98.2877 | 76.1047 | 287 | 2 | 287 | 5 | 4 | 80.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.2366 | 99.7807 | 98.6985 | 70.3346 | 910 | 2 | 910 | 12 | 9 | 75.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6954 | 99.5943 | 99.7967 | 57.4026 | 491 | 2 | 491 | 1 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 98.7562 | 99.4987 | 98.0247 | 65.4437 | 397 | 2 | 397 | 8 | 6 | 75.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 94.3396 | 98.4252 | 90.5797 | 53.8462 | 125 | 2 | 125 | 13 | 12 | 92.3077 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_51to200 | het | 95.5702 | 98.7805 | 92.5620 | 88.2296 | 162 | 2 | 112 | 9 | 7 | 77.7778 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | het | 77.4194 | 75.0000 | 80.0000 | 92.5373 | 6 | 2 | 4 | 1 | 1 | 100.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 95.8333 | 92.0000 | 100.0000 | 44.4444 | 23 | 2 | 25 | 0 | 0 | ||
| dgrover-gatk | INDEL | D16_PLUS | map_l100_m0_e0 | het | 82.2995 | 89.4737 | 76.1905 | 96.8278 | 17 | 2 | 16 | 5 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | map_l125_m2_e1 | * | 89.6552 | 92.8571 | 86.6667 | 97.2653 | 26 | 2 | 26 | 4 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | map_l150_m2_e1 | * | 86.4865 | 88.8889 | 84.2105 | 97.3973 | 16 | 2 | 16 | 3 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | segdup | * | 92.5620 | 96.5517 | 88.8889 | 96.4467 | 56 | 2 | 56 | 7 | 2 | 28.5714 | |
| dgrover-gatk | INDEL | D16_PLUS | segdup | hetalt | 87.5000 | 77.7778 | 100.0000 | 93.1818 | 7 | 2 | 9 | 0 | 0 | ||
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 99.7250 | 99.6337 | 99.8165 | 77.9531 | 544 | 2 | 544 | 1 | 1 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 75.4098 | 97.1831 | 61.6071 | 52.3404 | 69 | 2 | 69 | 43 | 43 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.6750 | 99.5671 | 99.7831 | 29.8326 | 460 | 2 | 460 | 1 | 1 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | map_l100_m0_e0 | hetalt | 88.8889 | 85.7143 | 92.3077 | 93.6275 | 12 | 2 | 12 | 1 | 0 | 0.0000 | |
| dgrover-gatk | INDEL | D1_5 | map_l150_m0_e0 | homalt | 98.2249 | 97.6471 | 98.8095 | 90.8795 | 83 | 2 | 83 | 1 | 1 | 100.0000 | |