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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
16451-16500 / 86044 show all | |||||||||||||||
| ndellapenna-hhga | SNP | ti | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 99.2625 | 98.9379 | 99.5892 | 62.6573 | 1211 | 13 | 1212 | 5 | 5 | 100.0000 | |
| ndellapenna-hhga | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.2708 | 98.9378 | 99.6061 | 37.1789 | 10618 | 114 | 10620 | 42 | 29 | 69.0476 | |
| gduggal-bwafb | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.4458 | 98.9378 | 97.9586 | 49.7551 | 10618 | 114 | 10653 | 222 | 58 | 26.1261 | |
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 98.4732 | 98.9378 | 98.0130 | 65.7049 | 12388 | 133 | 12233 | 248 | 237 | 95.5645 | |
| jli-custom | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.3263 | 98.9377 | 99.7181 | 59.8869 | 10990 | 118 | 10964 | 31 | 12 | 38.7097 | |
| cchapple-custom | SNP | tv | HG002compoundhet | homalt | 99.4506 | 98.9374 | 99.9692 | 37.6656 | 3352 | 36 | 3246 | 1 | 1 | 100.0000 | |
| gduggal-snapfb | SNP | tv | map_siren | het | 97.7974 | 98.9374 | 96.6834 | 63.5849 | 28305 | 304 | 28306 | 971 | 266 | 27.3944 | |
| hfeng-pmm1 | SNP | * | map_l125_m2_e1 | het | 99.2688 | 98.9372 | 99.6025 | 71.5784 | 29325 | 315 | 29319 | 117 | 29 | 24.7863 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 98.6759 | 98.9370 | 98.4161 | 73.8431 | 30156 | 324 | 29701 | 478 | 383 | 80.1255 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 98.6759 | 98.9370 | 98.4161 | 73.8431 | 30156 | 324 | 29701 | 478 | 383 | 80.1255 | |
| ckim-vqsr | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.3592 | 98.9362 | 99.7859 | 69.6359 | 465 | 5 | 466 | 1 | 1 | 100.0000 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 98.8822 | 98.9362 | 98.8283 | 47.8545 | 3627 | 39 | 3627 | 43 | 30 | 69.7674 | |
| ckim-vqsr | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.6913 | 98.9362 | 92.6526 | 62.3535 | 744 | 8 | 744 | 59 | 58 | 98.3051 | |
| dgrover-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.9381 | 98.9362 | 93.1164 | 62.2579 | 744 | 8 | 744 | 55 | 55 | 100.0000 | |
| ckim-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.6913 | 98.9362 | 92.6526 | 62.3535 | 744 | 8 | 744 | 59 | 58 | 98.3051 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.2714 | 98.9362 | 99.6089 | 56.7644 | 465 | 5 | 764 | 3 | 2 | 66.6667 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.2454 | 98.9362 | 99.5565 | 60.8846 | 465 | 5 | 449 | 2 | 0 | 0.0000 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.6913 | 98.9362 | 92.6526 | 62.5292 | 744 | 8 | 744 | 59 | 59 | 100.0000 | |
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.6298 | 98.9362 | 92.5373 | 61.3647 | 744 | 8 | 744 | 60 | 60 | 100.0000 | |
| hfeng-pmm1 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 95.8763 | 98.9362 | 93.0000 | 65.6947 | 186 | 2 | 186 | 14 | 13 | 92.8571 | |
| hfeng-pmm1 | SNP | * | map_l150_m0_e0 | * | 99.0843 | 98.9362 | 99.2329 | 79.6567 | 11904 | 128 | 11901 | 92 | 18 | 19.5652 | |
| hfeng-pmm1 | SNP | ti | map_l250_m2_e1 | * | 99.0337 | 98.9362 | 99.1315 | 88.6771 | 5022 | 54 | 5022 | 44 | 10 | 22.7273 | |
| jlack-gatk | INDEL | D16_PLUS | * | homalt | 98.8194 | 98.9362 | 98.7028 | 69.0115 | 1674 | 18 | 1674 | 22 | 15 | 68.1818 | |
| jli-custom | INDEL | I1_5 | lowcmp_SimpleRepeat_triTR_11to50 | het | 99.3590 | 98.9362 | 99.7854 | 67.0205 | 465 | 5 | 465 | 1 | 1 | 100.0000 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 95.8763 | 98.9362 | 93.0000 | 62.1928 | 744 | 8 | 744 | 56 | 55 | 98.2143 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 94.5362 | 98.9362 | 90.5109 | 61.6962 | 744 | 8 | 744 | 78 | 78 | 100.0000 | |
| ndellapenna-hhga | INDEL | I1_5 | * | * | 99.2393 | 98.9360 | 99.5445 | 55.9242 | 149061 | 1603 | 149032 | 682 | 431 | 63.1965 | |
| hfeng-pmm3 | SNP | * | map_l250_m2_e1 | * | 99.0226 | 98.9358 | 99.1095 | 88.7342 | 7902 | 85 | 7902 | 71 | 9 | 12.6761 | |
| jlack-gatk | SNP | tv | map_l100_m2_e1 | homalt | 99.4059 | 98.9357 | 99.8806 | 62.6933 | 9203 | 99 | 9203 | 11 | 7 | 63.6364 | |
| egarrison-hhga | SNP | * | map_l100_m1_e0 | het | 99.3656 | 98.9352 | 99.7999 | 63.8790 | 44876 | 483 | 44877 | 90 | 31 | 34.4444 | |
| hfeng-pmm3 | SNP | * | map_l250_m2_e0 | * | 99.0163 | 98.9347 | 99.0981 | 88.6629 | 7801 | 84 | 7801 | 71 | 9 | 12.6761 | |
| hfeng-pmm1 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 99.4644 | 98.9346 | 100.0000 | 77.9885 | 650 | 7 | 650 | 0 | 0 | ||
| gduggal-snapvard | SNP | * | * | * | 99.0871 | 98.9341 | 99.2406 | 23.7872 | 3022073 | 32560 | 3000636 | 22962 | 3691 | 16.0744 | |
| hfeng-pmm2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 99.4641 | 98.9339 | 100.0000 | 86.2965 | 464 | 5 | 464 | 0 | 0 | ||
| ndellapenna-hhga | INDEL | D1_5 | HG002complexvar | homalt | 98.4078 | 98.9338 | 97.8875 | 56.5863 | 10485 | 113 | 10472 | 226 | 169 | 74.7788 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.0945 | 98.9337 | 99.2558 | 72.1244 | 63744 | 687 | 63755 | 478 | 442 | 92.4686 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 99.2241 | 98.9337 | 99.5161 | 74.5848 | 63744 | 687 | 63757 | 310 | 273 | 88.0645 | |
| asubramanian-gatk | SNP | ti | lowcmp_SimpleRepeat_diTR_11to50 | homalt | 99.4640 | 98.9336 | 100.0000 | 64.4882 | 1670 | 18 | 1679 | 0 | 0 | ||
| jpowers-varprowl | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 97.9586 | 98.9331 | 97.0031 | 50.6413 | 17989 | 194 | 18029 | 557 | 149 | 26.7504 | |
| ndellapenna-hhga | SNP | tv | map_l250_m2_e0 | homalt | 99.3569 | 98.9328 | 99.7847 | 86.9321 | 927 | 10 | 927 | 2 | 2 | 100.0000 | |
| egarrison-hhga | SNP | * | map_l150_m2_e0 | * | 99.3568 | 98.9326 | 99.7847 | 74.8691 | 31512 | 340 | 31512 | 68 | 32 | 47.0588 | |
| asubramanian-gatk | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 98.6773 | 98.9323 | 98.4237 | 61.2579 | 55037 | 594 | 55072 | 882 | 34 | 3.8549 | |
| dgrover-gatk | SNP | tv | map_l125_m0_e0 | het | 98.4509 | 98.9321 | 97.9743 | 81.0960 | 4354 | 47 | 4353 | 90 | 15 | 16.6667 | |
| hfeng-pmm3 | SNP | tv | map_l125_m0_e0 | het | 99.0220 | 98.9321 | 99.1120 | 76.4302 | 4354 | 47 | 4353 | 39 | 3 | 7.6923 | |
| ltrigg-rtg2 | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.4631 | 98.9319 | 100.0000 | 77.5605 | 1482 | 16 | 1503 | 0 | 0 | ||
| ltrigg-rtg2 | SNP | ti | HG002compoundhet | homalt | 99.4222 | 98.9316 | 99.9177 | 28.6749 | 7315 | 79 | 7282 | 6 | 5 | 83.3333 | |
| ltrigg-rtg1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 97.7774 | 98.9308 | 96.6505 | 72.2034 | 28405 | 307 | 28740 | 996 | 22 | 2.2088 | |
| ltrigg-rtg1 | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 97.7774 | 98.9308 | 96.6505 | 72.2034 | 28405 | 307 | 28740 | 996 | 22 | 2.2088 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | homalt | 98.5303 | 98.9305 | 98.1333 | 57.4347 | 370 | 4 | 368 | 7 | 4 | 57.1429 | |
| ltrigg-rtg2 | SNP | tv | HG002compoundhet | het | 99.1949 | 98.9300 | 99.4612 | 50.0484 | 4623 | 50 | 4615 | 25 | 5 | 20.0000 | |