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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
20301-20350 / 86044 show all | |||||||||||||||
| hfeng-pmm1 | INDEL | D6_15 | HG002complexvar | homalt | 99.5730 | 99.7434 | 99.4032 | 61.2103 | 1166 | 3 | 1166 | 7 | 7 | 100.0000 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 97.3621 | 99.0244 | 95.7547 | 90.6402 | 203 | 2 | 203 | 9 | 7 | 77.7778 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 97.3621 | 99.0244 | 95.7547 | 90.6402 | 203 | 2 | 203 | 9 | 7 | 77.7778 | |
| hfeng-pmm1 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.9595 | 93.9583 | 98.0477 | 81.2678 | 451 | 29 | 452 | 9 | 7 | 77.7778 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 91.4634 | 91.4634 | 91.4634 | 76.4368 | 75 | 7 | 75 | 7 | 7 | 100.0000 | |
| hfeng-pmm3 | SNP | tv | map_siren | het | 99.6834 | 99.6155 | 99.7514 | 57.1444 | 28499 | 110 | 28494 | 71 | 7 | 9.8592 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | homalt | 99.8937 | 99.8584 | 99.9291 | 56.1359 | 11280 | 16 | 11280 | 8 | 7 | 87.5000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.7214 | 99.8141 | 99.6289 | 46.6996 | 2148 | 4 | 2148 | 8 | 7 | 87.5000 | |
| jlack-gatk | INDEL | * | lowcmp_SimpleRepeat_triTR_51to200 | * | 94.4550 | 92.3423 | 96.6667 | 63.0282 | 205 | 17 | 203 | 7 | 7 | 100.0000 | |
| jlack-gatk | INDEL | * | segdup | het | 92.8494 | 98.6357 | 87.7044 | 96.3215 | 1446 | 20 | 1448 | 203 | 7 | 3.4483 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.7688 | 94.2040 | 99.4772 | 35.3452 | 1219 | 75 | 1332 | 7 | 7 | 100.0000 | |
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 97.4121 | 96.3255 | 98.5235 | 67.0062 | 734 | 28 | 734 | 11 | 7 | 63.6364 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 88.1690 | 79.1569 | 99.4968 | 31.0362 | 1352 | 356 | 1384 | 7 | 7 | 100.0000 | |
| jlack-gatk | INDEL | I16_PLUS | * | hetalt | 92.9357 | 87.1306 | 99.5697 | 57.5280 | 1828 | 270 | 1851 | 8 | 7 | 87.5000 | |
| jlack-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 86.2745 | 100.0000 | 75.8621 | 86.5116 | 22 | 0 | 22 | 7 | 7 | 100.0000 | |
| hfeng-pmm2 | INDEL | D16_PLUS | HG002complexvar | het | 95.7182 | 93.4959 | 98.0488 | 66.5579 | 1035 | 72 | 804 | 16 | 7 | 43.7500 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 95.7529 | 97.6378 | 93.9394 | 49.0347 | 124 | 3 | 124 | 8 | 7 | 87.5000 | |
| hfeng-pmm2 | INDEL | D1_5 | HG002complexvar | homalt | 99.8773 | 99.8396 | 99.9150 | 58.5881 | 10581 | 17 | 10585 | 9 | 7 | 77.7778 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 94.5968 | 91.5493 | 97.8541 | 75.8173 | 455 | 42 | 456 | 10 | 7 | 70.0000 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.5238 | 93.1587 | 98.0122 | 81.7675 | 640 | 47 | 641 | 13 | 7 | 53.8462 | |
| hfeng-pmm2 | INDEL | I16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.8396 | 93.5417 | 98.2533 | 81.8470 | 449 | 31 | 450 | 8 | 7 | 87.5000 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 95.4633 | 93.6556 | 97.3422 | 77.2830 | 620 | 42 | 586 | 16 | 7 | 43.7500 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.1836 | 98.6234 | 99.7502 | 77.6187 | 6018 | 84 | 5989 | 15 | 7 | 46.6667 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 93.2118 | 90.9722 | 95.5645 | 79.3505 | 262 | 26 | 237 | 11 | 7 | 63.6364 | |
| hfeng-pmm2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.0393 | 99.2995 | 98.7805 | 65.9953 | 567 | 4 | 567 | 7 | 7 | 100.0000 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.9533 | 95.6873 | 98.2533 | 72.2760 | 710 | 32 | 675 | 12 | 7 | 58.3333 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 97.0630 | 95.6476 | 98.5210 | 73.1357 | 901 | 41 | 866 | 13 | 7 | 53.8462 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 99.4843 | 99.6244 | 99.3446 | 67.0980 | 1061 | 4 | 1061 | 7 | 7 | 100.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.7867 | 94.2786 | 99.4318 | 62.0564 | 2274 | 138 | 2275 | 13 | 7 | 53.8462 | |
| hfeng-pmm1 | SNP | * | map_l150_m0_e0 | homalt | 99.5848 | 99.7065 | 99.4633 | 76.6851 | 4077 | 12 | 4077 | 22 | 7 | 31.8182 | |
| hfeng-pmm1 | SNP | ti | map_l125_m1_e0 | homalt | 99.8143 | 99.7827 | 99.8460 | 66.1307 | 11021 | 24 | 11021 | 17 | 7 | 41.1765 | |
| hfeng-pmm1 | SNP | ti | map_l125_m2_e0 | homalt | 99.8195 | 99.7887 | 99.8502 | 68.6124 | 11334 | 24 | 11334 | 17 | 7 | 41.1765 | |
| hfeng-pmm1 | SNP | ti | map_l125_m2_e1 | homalt | 99.8210 | 99.7905 | 99.8515 | 68.6411 | 11434 | 24 | 11434 | 17 | 7 | 41.1765 | |
| hfeng-pmm1 | SNP | tv | HG002compoundhet | * | 97.0546 | 94.3517 | 99.9169 | 46.7711 | 8419 | 504 | 8417 | 7 | 7 | 100.0000 | |
| hfeng-pmm1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 99.0389 | 98.3049 | 99.7840 | 74.1160 | 14324 | 247 | 14324 | 31 | 7 | 22.5806 | |
| hfeng-pmm1 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 99.0389 | 98.3049 | 99.7840 | 74.1160 | 14324 | 247 | 14324 | 31 | 7 | 22.5806 | |
| hfeng-pmm1 | SNP | tv | map_l250_m2_e0 | * | 98.5906 | 98.2998 | 98.8831 | 88.2437 | 2833 | 49 | 2833 | 32 | 7 | 21.8750 | |
| hfeng-pmm1 | SNP | tv | map_l250_m2_e1 | * | 98.6071 | 98.3196 | 98.8962 | 88.3190 | 2867 | 49 | 2867 | 32 | 7 | 21.8750 | |
| hfeng-pmm2 | INDEL | * | HG002complexvar | hetalt | 97.5479 | 95.4312 | 99.7606 | 69.1784 | 3530 | 169 | 3750 | 9 | 7 | 77.7778 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.9418 | 94.1095 | 99.9498 | 41.0630 | 15721 | 984 | 15938 | 8 | 7 | 87.5000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 98.6376 | 98.7722 | 98.5034 | 72.1591 | 724 | 9 | 724 | 11 | 7 | 63.6364 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 99.2445 | 98.8084 | 99.6845 | 73.8057 | 5058 | 61 | 5056 | 16 | 7 | 43.7500 | |
| hfeng-pmm2 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.9418 | 94.1095 | 99.9498 | 41.0630 | 15721 | 984 | 15938 | 8 | 7 | 87.5000 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 98.3740 | 98.3740 | 98.3740 | 59.0341 | 484 | 8 | 484 | 8 | 7 | 87.5000 | |
| hfeng-pmm2 | INDEL | * | map_l100_m1_e0 | het | 98.0433 | 98.4787 | 97.6117 | 85.3524 | 2201 | 34 | 2207 | 54 | 7 | 12.9630 | |
| hfeng-pmm2 | INDEL | * | map_l100_m2_e0 | het | 98.0384 | 98.4395 | 97.6405 | 86.1291 | 2271 | 36 | 2276 | 55 | 7 | 12.7273 | |
| hfeng-pmm2 | INDEL | * | map_l100_m2_e1 | het | 98.0684 | 98.4635 | 97.6764 | 86.2047 | 2307 | 36 | 2312 | 55 | 7 | 12.7273 | |
| hfeng-pmm2 | INDEL | * | map_l125_m1_e0 | * | 98.2517 | 98.5762 | 97.9294 | 87.1694 | 2077 | 30 | 2081 | 44 | 7 | 15.9091 | |
| hfeng-pmm2 | INDEL | * | map_l125_m2_e0 | * | 98.2547 | 98.5883 | 97.9233 | 87.9829 | 2165 | 31 | 2169 | 46 | 7 | 15.2174 | |
| hfeng-pmm2 | INDEL | * | map_l125_m2_e1 | * | 98.2545 | 98.5618 | 97.9492 | 88.0799 | 2193 | 32 | 2197 | 46 | 7 | 15.2174 | |