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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
75751-75800 / 86044 show all | |||||||||||||||
| jmaeng-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 95.8065 | 92.2605 | 99.6360 | 30.7769 | 12946 | 1086 | 13139 | 48 | 48 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | HG002complexvar | * | 97.6527 | 96.5862 | 98.7430 | 52.4974 | 5121 | 181 | 4949 | 63 | 48 | 76.1905 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.1173 | 93.0761 | 99.3641 | 35.8818 | 7501 | 558 | 7500 | 48 | 48 | 100.0000 | |
| ltrigg-rtg1 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.1173 | 93.0761 | 99.3641 | 35.8818 | 7501 | 558 | 7500 | 48 | 48 | 100.0000 | |
| ltrigg-rtg1 | INDEL | I1_5 | HG002complexvar | * | 99.2488 | 98.7471 | 99.7557 | 52.7857 | 32944 | 418 | 32259 | 79 | 48 | 60.7595 | |
| jpowers-varprowl | INDEL | * | map_l150_m1_e0 | het | 92.1648 | 92.8655 | 91.4747 | 91.4533 | 794 | 61 | 794 | 74 | 48 | 64.8649 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.1646 | 92.9308 | 99.6316 | 30.7725 | 12791 | 973 | 12982 | 48 | 48 | 100.0000 | |
| bgallagher-sentieon | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 96.1489 | 92.9019 | 99.6311 | 33.4986 | 13036 | 996 | 13232 | 49 | 48 | 97.9592 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.6420 | 98.4090 | 98.8761 | 66.2789 | 19546 | 316 | 20235 | 230 | 48 | 20.8696 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | het | 81.4677 | 70.5559 | 96.3720 | 80.0416 | 2310 | 964 | 2311 | 87 | 48 | 55.1724 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 88.1401 | 80.0632 | 98.0294 | 59.0247 | 2534 | 631 | 2537 | 51 | 48 | 94.1176 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 78.1600 | 65.8800 | 96.0669 | 59.7785 | 3908 | 2024 | 3908 | 160 | 48 | 30.0000 | |
| gduggal-bwafb | SNP | tv | map_l100_m1_e0 | het | 98.4524 | 99.0335 | 97.8781 | 70.7160 | 15268 | 149 | 15268 | 331 | 48 | 14.5015 | |
| gduggal-bwafb | SNP | tv | map_l100_m2_e0 | het | 98.4689 | 99.0556 | 97.8891 | 72.5475 | 15628 | 149 | 15628 | 337 | 48 | 14.2433 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 53.6602 | 38.0295 | 91.1060 | 74.8783 | 799 | 1302 | 799 | 78 | 48 | 61.5385 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 73.7801 | 62.4350 | 90.1639 | 54.2729 | 600 | 361 | 550 | 60 | 48 | 80.0000 | |
| eyeh-varpipe | INDEL | D6_15 | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 83.2380 | 80.8271 | 85.7971 | 78.5980 | 215 | 51 | 296 | 49 | 48 | 97.9592 | |
| eyeh-varpipe | INDEL | D6_15 | map_l100_m2_e1 | * | 76.5753 | 70.9091 | 83.2258 | 83.8877 | 195 | 80 | 258 | 52 | 48 | 92.3077 | |
| eyeh-varpipe | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 49.6674 | 33.2688 | 97.9463 | 41.1847 | 1546 | 3101 | 2480 | 52 | 48 | 92.3077 | |
| gduggal-bwavard | INDEL | * | map_l150_m2_e1 | het | 89.0053 | 98.5931 | 81.1170 | 93.2572 | 911 | 13 | 915 | 213 | 48 | 22.5352 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m1_e0 | het | 92.3518 | 98.9247 | 86.5979 | 88.3812 | 1196 | 13 | 1176 | 182 | 48 | 26.3736 | |
| gduggal-bwavard | INDEL | D1_5 | map_l100_m2_e0 | het | 92.5331 | 98.8057 | 87.0093 | 88.9275 | 1241 | 15 | 1219 | 182 | 48 | 26.3736 | |
| gduggal-bwavard | INDEL | D6_15 | segdup | * | 68.8950 | 65.9686 | 72.0930 | 94.5707 | 126 | 65 | 124 | 48 | 48 | 100.0000 | |
| gduggal-bwavard | INDEL | D6_15 | segdup | het | 77.0066 | 95.6522 | 64.4444 | 95.1837 | 88 | 4 | 87 | 48 | 48 | 100.0000 | |
| gduggal-bwavard | SNP | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 93.9826 | 95.8648 | 92.1728 | 78.1956 | 4567 | 197 | 4522 | 384 | 48 | 12.5000 | |
| ckim-isaac | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | * | 83.8622 | 76.0787 | 93.4198 | 53.8889 | 1005 | 316 | 1008 | 71 | 48 | 67.6056 | |
| ckim-isaac | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 96.4572 | 94.0150 | 99.0295 | 31.3640 | 7006 | 446 | 7041 | 69 | 48 | 69.5652 | |
| dgrover-gatk | INDEL | I6_15 | HG002compoundhet | het | 86.2668 | 98.0769 | 76.9953 | 84.5091 | 204 | 4 | 164 | 49 | 48 | 97.9592 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.8137 | 96.5992 | 99.0592 | 63.6797 | 6107 | 215 | 6107 | 58 | 48 | 82.7586 | |
| dgrover-gatk | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.8137 | 96.5992 | 99.0592 | 63.6797 | 6107 | 215 | 6107 | 58 | 48 | 82.7586 | |
| dgrover-gatk | SNP | * | map_l100_m0_e0 | het | 99.0469 | 99.2549 | 98.8398 | 75.0691 | 21047 | 158 | 21043 | 247 | 48 | 19.4332 | |
| dgrover-gatk | SNP | * | map_l125_m0_e0 | * | 98.9327 | 98.9889 | 98.8765 | 77.4655 | 19189 | 196 | 19186 | 218 | 48 | 22.0183 | |
| egarrison-hhga | INDEL | D1_5 | HG002compoundhet | hetalt | 77.6385 | 63.8117 | 99.1149 | 65.8609 | 6519 | 3697 | 6159 | 55 | 48 | 87.2727 | |
| egarrison-hhga | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 97.9478 | 97.9351 | 97.9605 | 73.1911 | 5976 | 126 | 5956 | 124 | 48 | 38.7097 | |
| ckim-isaac | INDEL | D1_5 | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 98.9925 | 98.5647 | 99.4241 | 53.5139 | 14558 | 212 | 14501 | 84 | 48 | 57.1429 | |
| ckim-isaac | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 94.2123 | 89.8860 | 98.9760 | 27.5881 | 4888 | 550 | 5123 | 53 | 48 | 90.5660 | |
| egarrison-hhga | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3357 | 98.9921 | 99.6817 | 59.1116 | 35062 | 357 | 35070 | 112 | 48 | 42.8571 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 99.4570 | 99.2695 | 99.6453 | 71.3824 | 16851 | 124 | 16855 | 60 | 48 | 80.0000 | |
| egarrison-hhga | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 99.4570 | 99.2695 | 99.6453 | 71.3824 | 16851 | 124 | 16855 | 60 | 48 | 80.0000 | |
| hfeng-pmm2 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 93.1774 | 93.6073 | 92.7515 | 79.6508 | 820 | 56 | 627 | 49 | 48 | 97.9592 | |
| hfeng-pmm1 | SNP | * | * | het | 99.9238 | 99.8812 | 99.9665 | 18.1036 | 1871361 | 2226 | 1871236 | 628 | 48 | 7.6433 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | * | 96.4824 | 96.4286 | 96.5363 | 69.2228 | 1728 | 64 | 1728 | 62 | 48 | 77.4194 | |
| hfeng-pmm2 | SNP | ti | * | homalt | 99.9915 | 99.9903 | 99.9927 | 16.7561 | 802960 | 78 | 802952 | 59 | 48 | 81.3559 | |
| ckim-gatk | SNP | * | map_l100_m0_e0 | * | 82.8691 | 71.9040 | 97.7802 | 83.9171 | 23614 | 9227 | 23610 | 536 | 48 | 8.9552 | |
| ckim-isaac | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | het | 88.0678 | 85.5096 | 90.7838 | 68.5024 | 1074 | 182 | 1054 | 107 | 48 | 44.8598 | |
| cchapple-custom | INDEL | * | map_l100_m1_e0 | * | 95.9601 | 96.4584 | 95.4668 | 83.7178 | 3459 | 127 | 3538 | 168 | 48 | 28.5714 | |
| ciseli-custom | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 41.3700 | 79.5535 | 27.9532 | 77.8018 | 677 | 174 | 717 | 1848 | 48 | 2.5974 | |
| ciseli-custom | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | het | 76.8078 | 93.2966 | 65.2719 | 67.9320 | 2881 | 207 | 2917 | 1552 | 48 | 3.0928 | |
| ckim-dragen | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | homalt | 89.8396 | 97.2973 | 83.4437 | 59.6257 | 252 | 7 | 252 | 50 | 48 | 96.0000 | |
| cchapple-custom | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 96.9093 | 94.7026 | 99.2213 | 43.0691 | 6543 | 366 | 6626 | 52 | 48 | 92.3077 | |