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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
71351-71400 / 86044 show all | |||||||||||||||
| jlack-gatk | INDEL | * | map_l100_m1_e0 | het | 93.6574 | 98.2103 | 89.5079 | 89.1540 | 2195 | 40 | 2201 | 258 | 20 | 7.7519 | |
| hfeng-pmm1 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 99.5198 | 99.6042 | 99.4355 | 71.4918 | 3523 | 14 | 3523 | 20 | 20 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D16_PLUS | HG002compoundhet | * | 95.5047 | 92.1828 | 99.0749 | 28.5997 | 2158 | 183 | 2142 | 20 | 20 | 100.0000 | |
| ltrigg-rtg2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.4453 | 97.6298 | 99.2746 | 55.5967 | 8197 | 199 | 8211 | 60 | 20 | 33.3333 | |
| ltrigg-rtg2 | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 91.3456 | 85.6266 | 97.8831 | 68.3472 | 977 | 164 | 971 | 21 | 20 | 95.2381 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 98.5556 | 97.4729 | 99.6627 | 53.9495 | 5747 | 149 | 5909 | 20 | 20 | 100.0000 | |
| ltrigg-rtg2 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 98.5556 | 97.4729 | 99.6627 | 53.9495 | 5747 | 149 | 5909 | 20 | 20 | 100.0000 | |
| mlin-fermikit | INDEL | D6_15 | map_siren | homalt | 82.5533 | 81.5385 | 83.5938 | 87.3892 | 106 | 24 | 107 | 21 | 20 | 95.2381 | |
| mlin-fermikit | INDEL | I1_5 | HG002complexvar | hetalt | 88.8775 | 80.8806 | 98.6292 | 68.2274 | 1396 | 330 | 1439 | 20 | 20 | 100.0000 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 94.3483 | 92.8571 | 95.8882 | 60.8247 | 585 | 45 | 583 | 25 | 20 | 80.0000 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 97.5982 | 96.9186 | 98.2874 | 71.4134 | 1321 | 42 | 1320 | 23 | 20 | 86.9565 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 91.2206 | 93.2203 | 89.3048 | 64.9813 | 165 | 12 | 167 | 20 | 20 | 100.0000 | |
| mlin-fermikit | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 72.5735 | 57.3752 | 98.7253 | 40.9262 | 1517 | 1127 | 1549 | 20 | 20 | 100.0000 | |
| ndellapenna-hhga | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 82.7487 | 71.4392 | 98.3125 | 49.4079 | 1916 | 766 | 1806 | 31 | 20 | 64.5161 | |
| ndellapenna-hhga | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 62.9939 | 46.2118 | 98.9156 | 35.8827 | 2513 | 2925 | 2098 | 23 | 20 | 86.9565 | |
| ndellapenna-hhga | INDEL | D6_15 | map_siren | * | 91.7468 | 91.3556 | 92.1415 | 83.5594 | 465 | 44 | 469 | 40 | 20 | 50.0000 | |
| ndellapenna-hhga | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 86.1423 | 94.2623 | 79.3103 | 80.9461 | 115 | 7 | 115 | 30 | 20 | 66.6667 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 93.6086 | 92.9919 | 94.2335 | 70.5102 | 690 | 52 | 670 | 41 | 20 | 48.7805 | |
| ndellapenna-hhga | SNP | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 99.2051 | 98.7842 | 99.6296 | 37.6999 | 11294 | 139 | 11296 | 42 | 20 | 47.6190 | |
| ndellapenna-hhga | SNP | ti | map_l125_m1_e0 | het | 98.8592 | 97.9689 | 99.7658 | 69.2090 | 17895 | 371 | 17895 | 42 | 20 | 47.6190 | |
| ndellapenna-hhga | SNP | ti | map_l125_m2_e0 | het | 98.8804 | 98.0239 | 99.7520 | 70.6633 | 18503 | 373 | 18503 | 46 | 20 | 43.4783 | |
| ndellapenna-hhga | SNP | ti | map_l125_m2_e1 | het | 98.8822 | 98.0248 | 99.7547 | 70.7116 | 18710 | 377 | 18710 | 46 | 20 | 43.4783 | |
| ndellapenna-hhga | SNP | ti | map_siren | homalt | 99.8244 | 99.7072 | 99.9418 | 51.3860 | 37805 | 111 | 37806 | 22 | 20 | 90.9091 | |
| ndellapenna-hhga | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.3259 | 98.9526 | 99.7019 | 63.0961 | 17384 | 184 | 17391 | 52 | 20 | 38.4615 | |
| ndellapenna-hhga | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 96.4386 | 95.2569 | 97.6499 | 83.7824 | 1205 | 60 | 1205 | 29 | 20 | 68.9655 | |
| qzeng-custom | INDEL | * | map_l125_m0_e0 | het | 81.0999 | 72.7428 | 91.6264 | 95.2483 | 427 | 160 | 569 | 52 | 20 | 38.4615 | |
| mlin-fermikit | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | hetalt | 81.8304 | 69.7614 | 98.9490 | 45.2532 | 1871 | 811 | 1883 | 20 | 20 | 100.0000 | |
| mlin-fermikit | INDEL | * | map_l250_m1_e0 | * | 52.1158 | 38.3607 | 81.2500 | 92.0966 | 117 | 188 | 117 | 27 | 20 | 74.0741 | |
| mlin-fermikit | INDEL | * | map_l250_m2_e0 | homalt | 60.5128 | 51.3043 | 73.7500 | 92.2854 | 59 | 56 | 59 | 21 | 20 | 95.2381 | |
| mlin-fermikit | INDEL | * | map_l250_m2_e1 | homalt | 60.9137 | 51.7241 | 74.0741 | 92.4791 | 60 | 56 | 60 | 21 | 20 | 95.2381 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | het | 94.4196 | 95.2703 | 93.5841 | 72.6227 | 423 | 21 | 423 | 29 | 20 | 68.9655 | |
| mlin-fermikit | INDEL | D16_PLUS | map_siren | * | 67.3567 | 71.3287 | 63.8037 | 92.7716 | 102 | 41 | 104 | 59 | 20 | 33.8983 | |
| mlin-fermikit | INDEL | D1_5 | * | hetalt | 80.4314 | 67.3987 | 99.7126 | 64.5076 | 6905 | 3340 | 6939 | 20 | 20 | 100.0000 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | het | 87.2528 | 88.5714 | 85.9729 | 64.5833 | 31 | 4 | 190 | 31 | 20 | 64.5161 | |
| qzeng-custom | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | homalt | 99.3593 | 99.4891 | 99.2298 | 79.0524 | 3895 | 20 | 3865 | 30 | 20 | 66.6667 | |
| qzeng-custom | SNP | * | map_l250_m2_e1 | homalt | 74.8704 | 60.3017 | 98.7211 | 89.3099 | 1639 | 1079 | 1621 | 21 | 20 | 95.2381 | |
| qzeng-custom | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 98.5273 | 99.1969 | 97.8668 | 72.2743 | 4817 | 39 | 4863 | 106 | 20 | 18.8679 | |
| raldana-dualsentieon | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.8701 | 98.1095 | 99.6426 | 59.5927 | 10898 | 210 | 10873 | 39 | 20 | 51.2821 | |
| qzeng-custom | INDEL | D1_5 | map_l100_m0_e0 | het | 86.9445 | 80.0338 | 95.1613 | 92.6675 | 473 | 118 | 531 | 27 | 20 | 74.0741 | |
| qzeng-custom | INDEL | I16_PLUS | * | hetalt | 79.3637 | 66.7779 | 97.7954 | 49.1480 | 1401 | 697 | 1109 | 25 | 20 | 80.0000 | |
| qzeng-custom | INDEL | I16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | het | 86.1163 | 83.9286 | 88.4211 | 59.0164 | 141 | 27 | 420 | 55 | 20 | 36.3636 | |
| qzeng-custom | INDEL | I1_5 | map_siren | het | 87.6104 | 81.4396 | 94.7930 | 85.2134 | 1369 | 312 | 1511 | 83 | 20 | 24.0964 | |
| jpowers-varprowl | INDEL | * | map_l150_m0_e0 | * | 92.9134 | 91.8288 | 94.0239 | 93.2052 | 472 | 42 | 472 | 30 | 20 | 66.6667 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 69.3125 | 68.9655 | 69.6629 | 88.8471 | 60 | 27 | 62 | 27 | 20 | 74.0741 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_homopolymer_6to10 | het | 76.2389 | 92.3077 | 64.9351 | 86.6087 | 48 | 4 | 50 | 27 | 20 | 74.0741 | |
| jpowers-varprowl | INDEL | D1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | homalt | 49.8505 | 34.5745 | 89.3103 | 71.9536 | 260 | 492 | 259 | 31 | 20 | 64.5161 | |
| jpowers-varprowl | INDEL | D1_5 | map_l150_m1_e0 | * | 93.8289 | 93.3054 | 94.3583 | 88.8610 | 669 | 48 | 669 | 40 | 20 | 50.0000 | |
| jpowers-varprowl | INDEL | D1_5 | map_l150_m2_e0 | het | 93.9597 | 95.3307 | 92.6276 | 90.5316 | 490 | 24 | 490 | 39 | 20 | 51.2821 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.0831 | 94.5752 | 97.6399 | 85.2261 | 1447 | 83 | 1448 | 35 | 20 | 57.1429 | |
| jmaeng-gatk | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.0831 | 94.5752 | 97.6399 | 85.2261 | 1447 | 83 | 1448 | 35 | 20 | 57.1429 | |