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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
5901-5950 / 86044 show all | |||||||||||||||
| mlin-fermikit | INDEL | * | map_l125_m1_e0 | homalt | 70.9025 | 67.0765 | 75.1914 | 80.2241 | 491 | 241 | 491 | 162 | 142 | 87.6543 | |
| mlin-fermikit | INDEL | D16_PLUS | HG002compoundhet | homalt | 7.6994 | 87.5000 | 4.0268 | 56.6860 | 7 | 1 | 6 | 143 | 142 | 99.3007 | |
| gduggal-snapplat | SNP | tv | * | homalt | 99.0993 | 98.3541 | 99.8560 | 22.6563 | 370916 | 6207 | 370887 | 535 | 142 | 26.5421 | |
| gduggal-snapfb | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 44.7458 | 92.9577 | 29.4643 | 46.0241 | 66 | 5 | 66 | 158 | 142 | 89.8734 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 59.1835 | 45.3355 | 85.2120 | 34.7503 | 277 | 334 | 824 | 143 | 142 | 99.3007 | |
| gduggal-snapplat | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 44.5932 | 32.0350 | 73.3458 | 78.2195 | 1793 | 3804 | 1563 | 568 | 142 | 25.0000 | |
| jpowers-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.3478 | 97.8970 | 92.9280 | 84.6485 | 6517 | 140 | 6557 | 499 | 142 | 28.4569 | |
| jmaeng-gatk | INDEL | I1_5 | * | het | 99.3909 | 99.5129 | 99.2691 | 62.3588 | 78656 | 385 | 78640 | 579 | 142 | 24.5250 | |
| ckim-isaac | INDEL | D16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 86.8178 | 81.4097 | 92.9955 | 56.2615 | 2899 | 662 | 2881 | 217 | 142 | 65.4378 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 79.4509 | 70.3322 | 91.2863 | 53.7682 | 2456 | 1036 | 1540 | 147 | 142 | 96.5986 | |
| gduggal-bwafb | SNP | * | map_l100_m1_e0 | het | 98.6881 | 99.0035 | 98.3746 | 69.4458 | 44907 | 452 | 44909 | 742 | 142 | 19.1375 | |
| gduggal-bwavard | SNP | ti | map_l100_m2_e0 | het | 95.6400 | 97.2699 | 94.0639 | 78.7568 | 29786 | 836 | 29537 | 1864 | 142 | 7.6180 | |
| eyeh-varpipe | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 61.3581 | 44.8472 | 97.1096 | 76.3054 | 4169 | 5127 | 5006 | 149 | 142 | 95.3020 | |
| eyeh-varpipe | SNP | * | * | homalt | 99.9696 | 99.9699 | 99.9693 | 17.3914 | 1179807 | 355 | 1154702 | 355 | 142 | 40.0000 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 95.2637 | 99.3096 | 91.5345 | 77.9592 | 30928 | 215 | 29962 | 2771 | 142 | 5.1245 | |
| eyeh-varpipe | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 95.2637 | 99.3096 | 91.5345 | 77.9592 | 30928 | 215 | 29962 | 2771 | 142 | 5.1245 | |
| gduggal-bwavard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 81.2556 | 88.9456 | 74.7895 | 89.6153 | 1569 | 195 | 1510 | 509 | 141 | 27.7014 | |
| gduggal-bwavard | SNP | * | map_l100_m0_e0 | * | 94.9074 | 97.4514 | 92.4929 | 77.7735 | 32004 | 837 | 31615 | 2566 | 141 | 5.4949 | |
| gduggal-bwavard | SNP | * | map_l150_m2_e0 | * | 94.9737 | 97.7584 | 92.3433 | 83.0785 | 31138 | 714 | 30742 | 2549 | 141 | 5.5316 | |
| eyeh-varpipe | INDEL | D16_PLUS | HG002complexvar | het | 67.4853 | 60.0723 | 76.9854 | 48.1513 | 665 | 442 | 475 | 142 | 141 | 99.2958 | |
| gduggal-snapplat | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 79.2090 | 80.0667 | 78.3696 | 91.0972 | 8648 | 2153 | 8681 | 2396 | 141 | 5.8848 | |
| ghariani-varprowl | INDEL | I6_15 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 65.9794 | 77.7328 | 57.3134 | 76.8487 | 192 | 55 | 192 | 143 | 141 | 98.6014 | |
| ghariani-varprowl | SNP | ti | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 88.9998 | 98.0021 | 81.5123 | 84.1232 | 6524 | 133 | 6565 | 1489 | 141 | 9.4694 | |
| gduggal-snapvard | INDEL | I16_PLUS | HG002complexvar | het | 3.1923 | 1.6541 | 45.5157 | 59.5648 | 11 | 654 | 203 | 243 | 141 | 58.0247 | |
| gduggal-snapvard | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 82.8096 | 94.2598 | 73.8399 | 86.2952 | 10181 | 620 | 10009 | 3546 | 141 | 3.9763 | |
| gduggal-snapvard | SNP | tv | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 93.0446 | 97.3019 | 89.1441 | 72.7080 | 17094 | 474 | 16957 | 2065 | 141 | 6.8281 | |
| rpoplin-dv42 | SNP | * | map_l100_m1_e0 | het | 99.2638 | 99.1402 | 99.3876 | 64.2170 | 44969 | 390 | 44957 | 277 | 141 | 50.9025 | |
| rpoplin-dv42 | SNP | * | map_l100_m2_e0 | het | 99.2759 | 99.1530 | 99.3992 | 65.9847 | 46006 | 393 | 45994 | 278 | 141 | 50.7194 | |
| anovak-vg | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | het | 40.2391 | 29.5082 | 63.2353 | 29.4815 | 36 | 86 | 301 | 175 | 141 | 80.5714 | |
| anovak-vg | SNP | tv | lowcmp_SimpleRepeat_quadTR_11to50 | * | 96.7152 | 97.3162 | 96.1216 | 41.6514 | 7252 | 200 | 7336 | 296 | 141 | 47.6351 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | het | 92.1502 | 94.7199 | 89.7161 | 77.6402 | 2063 | 115 | 1928 | 221 | 141 | 63.8009 | |
| asubramanian-gatk | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | homalt | 79.7448 | 96.1003 | 68.1467 | 47.3577 | 345 | 14 | 353 | 165 | 141 | 85.4545 | |
| astatham-gatk | INDEL | I1_5 | * | het | 99.5857 | 99.4610 | 99.7107 | 60.4880 | 78615 | 426 | 78596 | 228 | 141 | 61.8421 | |
| cchapple-custom | INDEL | D1_5 | HG002compoundhet | homalt | 73.8232 | 98.6254 | 58.9888 | 82.3150 | 287 | 4 | 210 | 146 | 141 | 96.5753 | |
| mlin-fermikit | INDEL | * | map_siren | het | 83.7074 | 75.1996 | 94.3858 | 76.9241 | 3390 | 1118 | 3396 | 202 | 141 | 69.8020 | |
| qzeng-custom | SNP | tv | HG002complexvar | homalt | 99.2146 | 98.6185 | 99.8179 | 23.3623 | 93797 | 1314 | 91543 | 167 | 141 | 84.4311 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 81.7913 | 85.3474 | 78.5196 | 66.0925 | 565 | 97 | 541 | 148 | 141 | 95.2703 | |
| mlin-fermikit | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | homalt | 87.7292 | 95.8398 | 80.8843 | 58.8109 | 622 | 27 | 622 | 147 | 141 | 95.9184 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 93.5222 | 92.4891 | 94.5785 | 50.7408 | 2549 | 207 | 2547 | 146 | 141 | 96.5753 | |
| jlack-gatk | SNP | ti | map_l100_m0_e0 | * | 96.2565 | 98.6312 | 93.9935 | 77.0428 | 21473 | 298 | 21470 | 1372 | 141 | 10.2770 | |
| jpowers-varprowl | SNP | * | map_l150_m0_e0 | * | 95.7982 | 95.3125 | 96.2888 | 84.7317 | 11468 | 564 | 11468 | 442 | 141 | 31.9005 | |
| jpowers-varprowl | SNP | ti | map_l150_m2_e1 | * | 97.3682 | 96.6752 | 98.0713 | 80.1400 | 20034 | 689 | 20034 | 394 | 141 | 35.7868 | |
| jpowers-varprowl | SNP | tv | map_l100_m2_e1 | * | 97.6564 | 97.6506 | 97.6622 | 73.7732 | 24689 | 594 | 24689 | 591 | 141 | 23.8579 | |
| jpowers-varprowl | SNP | ti | map_l150_m1_e0 | * | 97.2860 | 96.5605 | 98.0225 | 78.7128 | 19034 | 678 | 19034 | 384 | 140 | 36.4583 | |
| jpowers-varprowl | SNP | ti | map_l150_m2_e0 | * | 97.3631 | 96.6654 | 98.0710 | 80.0739 | 19828 | 684 | 19828 | 390 | 140 | 35.8974 | |
| jpowers-varprowl | SNP | tv | map_l100_m2_e0 | * | 97.6510 | 97.6471 | 97.6549 | 73.7409 | 24444 | 589 | 24444 | 587 | 140 | 23.8501 | |
| jmaeng-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | * | 83.6527 | 80.4403 | 87.1324 | 45.1060 | 950 | 231 | 948 | 140 | 140 | 100.0000 | |
| jli-custom | INDEL | I1_5 | * | homalt | 99.8065 | 99.8527 | 99.7603 | 53.8126 | 60339 | 89 | 60343 | 145 | 140 | 96.5517 | |
| ciseli-custom | INDEL | I16_PLUS | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 17.4295 | 10.9553 | 42.6117 | 84.6357 | 125 | 1016 | 124 | 167 | 140 | 83.8323 | |
| rpoplin-dv42 | INDEL | I16_PLUS | * | * | 94.2741 | 91.2655 | 97.4879 | 59.7696 | 5820 | 557 | 5821 | 150 | 140 | 93.3333 | |