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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
18101-18150 / 86044 show all | |||||||||||||||
| egarrison-hhga | INDEL | * | map_l150_m2_e0 | * | 97.7239 | 97.5142 | 97.9345 | 98.6965 | 1373 | 35 | 1375 | 29 | 10 | 34.4828 | |
| egarrison-hhga | INDEL | * | map_l150_m2_e1 | * | 97.7374 | 97.4983 | 97.9777 | 98.7042 | 1403 | 36 | 1405 | 29 | 10 | 34.4828 | |
| dgrover-gatk | INDEL | I16_PLUS | * | het | 98.6296 | 98.3076 | 98.9537 | 76.0151 | 2672 | 46 | 2648 | 28 | 9 | 32.1429 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 97.5138 | 96.0416 | 99.0318 | 51.5497 | 2863 | 118 | 2864 | 28 | 23 | 82.1429 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 95.6923 | 100.0000 | 91.7404 | 70.4446 | 311 | 0 | 311 | 28 | 27 | 96.4286 | |
| egarrison-hhga | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 81.6150 | 69.6868 | 98.4699 | 49.2653 | 1869 | 813 | 1802 | 28 | 24 | 85.7143 | |
| ckim-isaac | SNP | ti | map_l150_m1_e0 | * | 71.6515 | 55.9050 | 99.7466 | 75.8793 | 11020 | 8692 | 11020 | 28 | 5 | 17.8571 | |
| ckim-isaac | SNP | tv | map_l125_m2_e0 | het | 74.7458 | 59.8353 | 99.5540 | 75.8427 | 6248 | 4194 | 6250 | 28 | 7 | 25.0000 | |
| ckim-isaac | SNP | tv | map_l125_m2_e1 | het | 74.8404 | 59.9545 | 99.5595 | 75.8491 | 6327 | 4226 | 6329 | 28 | 7 | 25.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | * | homalt | 99.0314 | 99.7045 | 98.3673 | 70.9863 | 1687 | 5 | 1687 | 28 | 22 | 78.5714 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 97.7255 | 97.6911 | 97.7600 | 78.8994 | 1227 | 29 | 1222 | 28 | 7 | 25.0000 | |
| dgrover-gatk | INDEL | * | map_l125_m1_e0 | het | 97.9822 | 98.0524 | 97.9120 | 89.0949 | 1309 | 26 | 1313 | 28 | 4 | 14.2857 | |
| dgrover-gatk | INDEL | * | map_l125_m2_e0 | het | 98.0266 | 98.0590 | 97.9943 | 89.7744 | 1364 | 27 | 1368 | 28 | 4 | 14.2857 | |
| dgrover-gatk | INDEL | * | map_l125_m2_e1 | het | 98.0504 | 98.0824 | 98.0184 | 89.8484 | 1381 | 27 | 1385 | 28 | 4 | 14.2857 | |
| dgrover-gatk | INDEL | * | map_l150_m1_e0 | * | 97.9486 | 97.9821 | 97.9151 | 90.7142 | 1311 | 27 | 1315 | 28 | 6 | 21.4286 | |
| dgrover-gatk | INDEL | * | map_l150_m2_e0 | * | 98.0504 | 98.0824 | 98.0184 | 91.3212 | 1381 | 27 | 1385 | 28 | 6 | 21.4286 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 98.4993 | 99.5404 | 97.4797 | 67.4289 | 1083 | 5 | 1083 | 28 | 22 | 78.5714 | |
| dgrover-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | het | 97.0995 | 99.3432 | 94.9550 | 83.9270 | 605 | 4 | 527 | 28 | 20 | 71.4286 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.7426 | 96.1442 | 99.3950 | 25.7739 | 4588 | 184 | 4600 | 28 | 27 | 96.4286 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 97.6925 | 98.3731 | 97.0213 | 73.9323 | 907 | 15 | 912 | 28 | 15 | 53.5714 | |
| egarrison-hhga | INDEL | D6_15 | HG002complexvar | hetalt | 65.3629 | 50.0494 | 94.1788 | 58.1739 | 507 | 506 | 453 | 28 | 24 | 85.7143 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | * | 70.3098 | 64.7887 | 76.8595 | 44.7489 | 92 | 50 | 93 | 28 | 26 | 92.8571 | |
| egarrison-hhga | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_51to200 | het | 60.4317 | 87.5000 | 46.1538 | 56.3025 | 21 | 3 | 24 | 28 | 26 | 92.8571 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 99.2393 | 99.5160 | 98.9641 | 59.7528 | 2673 | 13 | 2675 | 28 | 4 | 14.2857 | |
| egarrison-hhga | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 93.5989 | 91.3889 | 95.9184 | 85.0610 | 658 | 62 | 658 | 28 | 8 | 28.5714 | |
| egarrison-hhga | SNP | ti | map_l125_m0_e0 | * | 99.2437 | 98.7149 | 99.7782 | 73.5653 | 12598 | 164 | 12598 | 28 | 14 | 50.0000 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 98.6910 | 99.5997 | 97.7987 | 75.1563 | 1244 | 5 | 1244 | 28 | 22 | 78.5714 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 96.7712 | 99.6205 | 94.0803 | 83.0466 | 525 | 2 | 445 | 28 | 26 | 92.8571 | |
| ckim-vqsr | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 98.6910 | 99.5997 | 97.7987 | 75.1563 | 1244 | 5 | 1244 | 28 | 22 | 78.5714 | |
| ckim-vqsr | INDEL | D1_5 | map_l100_m0_e0 | het | 96.0537 | 96.7851 | 95.3333 | 90.9829 | 572 | 19 | 572 | 28 | 2 | 7.1429 | |
| ckim-vqsr | INDEL | D6_15 | HG002complexvar | het | 98.8682 | 98.6538 | 99.0835 | 59.5418 | 3078 | 42 | 3027 | 28 | 22 | 78.5714 | |
| ckim-vqsr | SNP | * | HG002complexvar | homalt | 98.2744 | 96.6168 | 99.9900 | 20.3688 | 278811 | 9763 | 278787 | 28 | 26 | 92.8571 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 86.0411 | 80.9896 | 91.7647 | 78.8951 | 311 | 73 | 312 | 28 | 8 | 28.5714 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 92.4298 | 90.2778 | 94.6869 | 59.3991 | 520 | 56 | 499 | 28 | 9 | 32.1429 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | * | 93.1635 | 90.0348 | 96.5174 | 56.7974 | 777 | 86 | 776 | 28 | 7 | 25.0000 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 92.2495 | 86.6245 | 98.6558 | 36.0651 | 2053 | 317 | 2055 | 28 | 21 | 75.0000 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_51to200 | * | 70.6147 | 60.2230 | 85.3403 | 77.0433 | 162 | 107 | 163 | 28 | 7 | 25.0000 | |
| gduggal-snapvard | INDEL | D1_5 | map_siren | homalt | 93.2963 | 89.3836 | 97.5673 | 70.4493 | 1044 | 124 | 1123 | 28 | 26 | 92.8571 | |
| gduggal-snapvard | INDEL | I6_15 | HG002complexvar | homalt | 45.0525 | 29.6785 | 93.4732 | 26.9165 | 360 | 853 | 401 | 28 | 27 | 96.4286 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 29.2460 | 17.8797 | 80.2817 | 70.2306 | 113 | 519 | 114 | 28 | 24 | 85.7143 | |
| ghariani-varprowl | INDEL | D1_5 | map_siren | homalt | 95.7280 | 94.0068 | 97.5133 | 74.2805 | 1098 | 70 | 1098 | 28 | 6 | 21.4286 | |
| gduggal-snapfb | INDEL | I6_15 | map_siren | * | 79.8374 | 72.4590 | 88.8889 | 71.7489 | 221 | 84 | 224 | 28 | 26 | 92.8571 | |
| gduggal-snapfb | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | hetalt | 0.0000 | 0.0000 | 73.8318 | 0 | 0 | 0 | 28 | 0 | 0.0000 | ||
| ghariani-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | homalt | 99.1063 | 99.9378 | 98.2885 | 58.1479 | 1608 | 1 | 1608 | 28 | 18 | 64.2857 | |
| ghariani-varprowl | SNP | tv | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 97.2067 | 99.6183 | 94.9091 | 73.8841 | 522 | 2 | 522 | 28 | 19 | 67.8571 | |
| ghariani-varprowl | SNP | tv | map_l150_m1_e0 | homalt | 98.6612 | 98.0487 | 99.2815 | 73.6565 | 3869 | 77 | 3869 | 28 | 15 | 53.5714 | |
| ghariani-varprowl | SNP | tv | map_l150_m2_e0 | homalt | 98.6939 | 98.0896 | 99.3057 | 75.8431 | 4005 | 78 | 4005 | 28 | 15 | 53.5714 | |
| ghariani-varprowl | SNP | tv | map_l150_m2_e1 | homalt | 98.7101 | 98.1132 | 99.3144 | 75.8171 | 4056 | 78 | 4056 | 28 | 15 | 53.5714 | |
| hfeng-pmm1 | INDEL | * | map_l100_m2_e0 | het | 97.7908 | 96.8357 | 98.7649 | 83.7444 | 2234 | 73 | 2239 | 28 | 4 | 14.2857 | |
| hfeng-pmm1 | INDEL | * | map_l100_m2_e1 | het | 97.8030 | 96.8417 | 98.7837 | 83.8513 | 2269 | 74 | 2274 | 28 | 4 | 14.2857 | |