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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
58101-58150 / 86044 show all | |||||||||||||||
| ckim-isaac | INDEL | D16_PLUS | map_l100_m2_e1 | het | 29.5567 | 19.6078 | 60.0000 | 94.2085 | 10 | 41 | 9 | 6 | 3 | 50.0000 | |
| ckim-isaac | INDEL | D16_PLUS | segdup | * | 86.7257 | 84.4828 | 89.0909 | 92.1090 | 49 | 9 | 49 | 6 | 3 | 50.0000 | |
| ckim-isaac | INDEL | D16_PLUS | segdup | het | 86.4020 | 89.1892 | 83.7838 | 91.6290 | 33 | 4 | 31 | 6 | 3 | 50.0000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 87.5378 | 78.4574 | 98.9950 | 44.8753 | 590 | 162 | 591 | 6 | 5 | 83.3333 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | hetalt | 87.1765 | 82.4324 | 92.5000 | 74.6032 | 61 | 13 | 74 | 6 | 6 | 100.0000 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 82.4610 | 70.7692 | 98.7805 | 27.7533 | 460 | 190 | 486 | 6 | 5 | 83.3333 | |
| ckim-isaac | INDEL | D1_5 | map_l150_m1_e0 | het | 79.8048 | 67.2199 | 98.1873 | 91.0516 | 324 | 158 | 325 | 6 | 2 | 33.3333 | |
| ckim-isaac | INDEL | D1_5 | map_l150_m2_e0 | het | 79.9092 | 67.3152 | 98.3003 | 91.4899 | 346 | 168 | 347 | 6 | 2 | 33.3333 | |
| ckim-isaac | INDEL | D1_5 | map_l150_m2_e1 | het | 79.5911 | 66.8582 | 98.3146 | 91.5439 | 349 | 173 | 350 | 6 | 2 | 33.3333 | |
| ckim-isaac | INDEL | D1_5 | segdup | het | 98.8393 | 98.5549 | 99.1254 | 93.5804 | 682 | 10 | 680 | 6 | 2 | 33.3333 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | homalt | 93.9237 | 90.0875 | 98.1013 | 46.7116 | 309 | 34 | 310 | 6 | 1 | 16.6667 | |
| ckim-isaac | INDEL | D6_15 | segdup | het | 89.7285 | 86.9565 | 92.6829 | 92.5319 | 80 | 12 | 76 | 6 | 6 | 100.0000 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 65.3856 | 51.5789 | 89.2857 | 85.3018 | 49 | 46 | 50 | 6 | 2 | 33.3333 | |
| ckim-isaac | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 69.0423 | 55.5556 | 91.1765 | 83.6145 | 60 | 48 | 62 | 6 | 2 | 33.3333 | |
| ckim-isaac | INDEL | I1_5 | map_l100_m2_e1 | het | 89.3559 | 81.3580 | 99.0977 | 86.3869 | 659 | 151 | 659 | 6 | 1 | 16.6667 | |
| ckim-isaac | INDEL | I1_5 | map_siren | homalt | 84.1104 | 72.9373 | 99.3258 | 73.3293 | 884 | 328 | 884 | 6 | 3 | 50.0000 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 81.5179 | 74.0741 | 90.6250 | 67.6768 | 60 | 21 | 58 | 6 | 2 | 33.3333 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.2480 | 97.5124 | 96.9849 | 88.9751 | 196 | 5 | 193 | 6 | 1 | 16.6667 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.4854 | 99.3353 | 99.6359 | 61.3327 | 1644 | 11 | 1642 | 6 | 3 | 50.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.6785 | 97.8849 | 99.4850 | 27.6398 | 1157 | 25 | 1159 | 6 | 6 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | hetalt | 97.2401 | 95.3342 | 99.2238 | 23.4653 | 756 | 37 | 767 | 6 | 6 | 100.0000 | |
| ckim-vqsr | INDEL | D6_15 | map_l100_m0_e0 | * | 95.6938 | 97.0874 | 94.3396 | 91.8147 | 100 | 3 | 100 | 6 | 1 | 16.6667 | |
| ckim-vqsr | INDEL | D6_15 | map_l100_m0_e0 | het | 94.4000 | 98.3333 | 90.7692 | 93.0851 | 59 | 1 | 59 | 6 | 1 | 16.6667 | |
| ckim-vqsr | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 91.9540 | 97.5610 | 86.9565 | 88.1748 | 40 | 1 | 40 | 6 | 6 | 100.0000 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.5020 | 96.0317 | 99.0180 | 65.9610 | 605 | 25 | 605 | 6 | 5 | 83.3333 | |
| ckim-vqsr | INDEL | I1_5 | map_l250_m1_e0 | het | 91.8033 | 93.3333 | 90.3226 | 98.0000 | 56 | 4 | 56 | 6 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | I1_5 | map_l250_m2_e0 | het | 91.7293 | 92.4242 | 91.0448 | 98.1295 | 61 | 5 | 61 | 6 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | I1_5 | map_l250_m2_e1 | het | 91.7293 | 92.4242 | 91.0448 | 98.1892 | 61 | 5 | 61 | 6 | 0 | 0.0000 | |
| ckim-vqsr | INDEL | I6_15 | * | hetalt | 95.9384 | 92.2582 | 99.9244 | 35.7201 | 7889 | 662 | 7930 | 6 | 5 | 83.3333 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 88.8889 | 100.0000 | 80.0000 | 79.4521 | 24 | 0 | 24 | 6 | 6 | 100.0000 | |
| ckim-vqsr | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.3114 | 97.6783 | 98.9529 | 73.0099 | 589 | 14 | 567 | 6 | 2 | 33.3333 | |
| ckim-vqsr | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5376 | 99.1089 | 99.9700 | 56.4901 | 20019 | 180 | 20019 | 6 | 6 | 100.0000 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 97.3822 | 96.3731 | 98.4127 | 91.0490 | 372 | 14 | 372 | 6 | 4 | 66.6667 | |
| ckim-vqsr | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 97.0803 | 96.3768 | 97.7941 | 91.0703 | 266 | 10 | 266 | 6 | 4 | 66.6667 | |
| ckim-vqsr | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 99.6562 | 99.3685 | 99.9455 | 58.6114 | 11014 | 70 | 11010 | 6 | 4 | 66.6667 | |
| 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_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 99.6878 | 99.7917 | 99.5842 | 69.2913 | 1437 | 3 | 1437 | 6 | 0 | 0.0000 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.6181 | 99.8906 | 99.3471 | 70.2781 | 913 | 1 | 913 | 6 | 0 | 0.0000 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 99.3666 | 99.2095 | 99.5242 | 88.1418 | 1255 | 10 | 1255 | 6 | 6 | 100.0000 | |
| ckim-vqsr | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | * | 99.7534 | 99.6812 | 99.8257 | 39.7409 | 3439 | 11 | 3436 | 6 | 2 | 33.3333 | |
| ckim-vqsr | SNP | tv | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.8363 | 99.9532 | 99.7196 | 42.4576 | 2137 | 1 | 2134 | 6 | 2 | 33.3333 | |
| dgrover-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 98.9101 | 98.0611 | 99.7739 | 42.7400 | 2630 | 52 | 2648 | 6 | 6 | 100.0000 | |
| dgrover-gatk | INDEL | * | map_l125_m0_e0 | homalt | 97.8873 | 97.8873 | 97.8873 | 88.7703 | 278 | 6 | 278 | 6 | 4 | 66.6667 | |
| dgrover-gatk | INDEL | * | map_l150_m1_e0 | homalt | 98.4816 | 98.2684 | 98.6957 | 88.7778 | 454 | 8 | 454 | 6 | 3 | 50.0000 | |
| dgrover-gatk | INDEL | * | map_l150_m2_e0 | homalt | 98.5417 | 98.3368 | 98.7474 | 89.6834 | 473 | 8 | 473 | 6 | 3 | 50.0000 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.2465 | 99.7835 | 98.7152 | 64.0769 | 461 | 1 | 461 | 6 | 6 | 100.0000 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 94.0410 | 89.1557 | 99.4928 | 31.2609 | 1151 | 140 | 1177 | 6 | 5 | 83.3333 | |
| ckim-isaac | SNP | * | func_cds | * | 99.4183 | 98.8760 | 99.9666 | 20.1352 | 17946 | 204 | 17946 | 6 | 2 | 33.3333 | |
| ckim-isaac | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 84.6065 | 77.2727 | 93.4783 | 86.4507 | 85 | 25 | 86 | 6 | 4 | 66.6667 | |