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 | |||||||||||||||
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 87.1382 | 78.3947 | 98.0769 | 64.9494 | 2852 | 786 | 2856 | 56 | 50 | 89.2857 | |
| asubramanian-gatk | INDEL | D1_5 | * | het | 99.3754 | 99.1025 | 99.6499 | 59.9427 | 86788 | 786 | 86804 | 305 | 126 | 41.3115 | |
| gduggal-snapplat | SNP | ti | map_l125_m0_e0 | het | 91.6658 | 90.4877 | 92.8749 | 86.7400 | 7477 | 786 | 7482 | 574 | 330 | 57.4913 | |
| ltrigg-rtg2 | SNP | * | map_l125_m2_e1 | het | 98.5451 | 97.3516 | 99.7684 | 58.0187 | 28855 | 785 | 28856 | 67 | 6 | 8.9552 | |
| jlack-gatk | INDEL | D6_15 | * | hetalt | 94.6900 | 90.3964 | 99.4119 | 33.6937 | 7389 | 785 | 7438 | 44 | 37 | 84.0909 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 94.6297 | 90.2717 | 99.4297 | 29.8103 | 7275 | 784 | 7323 | 42 | 36 | 85.7143 | |
| jlack-gatk | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 94.6297 | 90.2717 | 99.4297 | 29.8103 | 7275 | 784 | 7323 | 42 | 36 | 85.7143 | |
| gduggal-snapplat | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 784 | 0 | 0 | 0 | |||
| gduggal-snapfb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 784 | 0 | 0 | 0 | |||
| gduggal-snapfb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_51to200bp_gt95identity_merged | * | 67.0995 | 63.6364 | 70.9612 | 72.1865 | 1372 | 784 | 1410 | 577 | 119 | 20.6239 | |
| ckim-gatk | INDEL | I6_15 | * | * | 97.6383 | 96.8416 | 98.4482 | 52.9059 | 24039 | 784 | 24044 | 379 | 335 | 88.3905 | |
| ckim-gatk | SNP | * | map_l250_m0_e0 | het | 63.7809 | 47.9416 | 95.2507 | 98.3918 | 722 | 784 | 722 | 36 | 2 | 5.5556 | |
| ckim-dragen | INDEL | * | * | het | 99.4503 | 99.5962 | 99.3048 | 61.2221 | 193349 | 784 | 192841 | 1350 | 335 | 24.8148 | |
| ltrigg-rtg2 | SNP | * | map_l125_m2_e0 | het | 98.5358 | 97.3259 | 99.7762 | 57.8912 | 28534 | 784 | 28535 | 64 | 6 | 9.3750 | |
| gduggal-snapvard | SNP | ti | map_l150_m1_e0 | * | 92.4318 | 96.0278 | 89.0953 | 81.2252 | 18929 | 783 | 18751 | 2295 | 187 | 8.1482 | |
| cchapple-custom | SNP | * | map_l125_m2_e1 | het | 96.1447 | 97.3583 | 94.9610 | 78.6712 | 28857 | 783 | 28890 | 1533 | 346 | 22.5701 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.3791 | 96.4809 | 98.2942 | 54.2906 | 21467 | 783 | 21493 | 373 | 326 | 87.3995 | |
| ltrigg-rtg2 | SNP | * | map_l125_m1_e0 | het | 98.5086 | 97.2457 | 99.8048 | 55.1586 | 27610 | 782 | 27610 | 54 | 6 | 11.1111 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | * | 81.7039 | 73.7672 | 91.5543 | 53.9843 | 2199 | 782 | 1290 | 119 | 114 | 95.7983 | |
| jpowers-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 0.2551 | 0.0000 | 0.0000 | 2 | 782 | 0 | 0 | 0 | ||
| jpowers-varprowl | SNP | * | map_l125_m0_e0 | * | 96.4836 | 95.9660 | 97.0068 | 80.1786 | 18603 | 782 | 18603 | 574 | 180 | 31.3589 | |
| gduggal-snapvard | INDEL | I1_5 | HG002complexvar | het | 90.2347 | 95.7007 | 85.3594 | 58.5913 | 17407 | 782 | 17730 | 3041 | 2197 | 72.2460 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 0.2551 | 0.0000 | 0.0000 | 2 | 782 | 0 | 0 | 0 | ||
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 77.3354 | 79.2618 | 75.5004 | 55.1018 | 2985 | 781 | 2980 | 967 | 964 | 99.6898 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 77.3354 | 79.2618 | 75.5004 | 55.1018 | 2985 | 781 | 2980 | 967 | 964 | 99.6898 | |
| gduggal-snapplat | SNP | ti | map_l250_m1_e0 | * | 88.1520 | 82.9439 | 94.0579 | 93.4361 | 3798 | 781 | 3799 | 240 | 126 | 52.5000 | |
| gduggal-bwafb | INDEL | I1_5 | * | homalt | 98.8253 | 98.7076 | 98.9433 | 52.6434 | 59647 | 781 | 59646 | 637 | 616 | 96.7033 | |
| eyeh-varpipe | INDEL | D6_15 | * | homalt | 70.9562 | 87.6541 | 59.6022 | 44.0635 | 5545 | 781 | 5543 | 3757 | 3655 | 97.2851 | |
| bgallagher-sentieon | INDEL | I1_5 | HG002compoundhet | * | 95.0768 | 93.6792 | 96.5167 | 65.8897 | 11575 | 781 | 11582 | 418 | 416 | 99.5215 | |
| eyeh-varpipe | INDEL | * | HG002compoundhet | het | 65.1467 | 80.9233 | 54.5181 | 69.0092 | 3313 | 781 | 1267 | 1057 | 968 | 91.5799 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.2283 | 95.5860 | 98.9279 | 54.0066 | 16891 | 780 | 16887 | 183 | 169 | 92.3497 | |
| hfeng-pmm2 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.2283 | 95.5860 | 98.9279 | 54.0066 | 16891 | 780 | 16887 | 183 | 169 | 92.3497 | |
| gduggal-bwafb | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 79.5287 | 70.4992 | 91.2109 | 53.4545 | 1864 | 780 | 467 | 45 | 45 | 100.0000 | |
| ltrigg-rtg1 | SNP | * | map_l100_m1_e0 | het | 98.9962 | 98.2804 | 99.7226 | 54.6285 | 44579 | 780 | 44576 | 124 | 12 | 9.6774 | |
| cchapple-custom | SNP | * | map_l125_m2_e0 | het | 96.1245 | 97.3395 | 94.9395 | 78.6207 | 28538 | 780 | 28573 | 1523 | 346 | 22.7183 | |
| ciseli-custom | SNP | * | map_l250_m0_e0 | * | 67.3632 | 63.4660 | 71.7703 | 95.4310 | 1355 | 780 | 1350 | 531 | 99 | 18.6441 | |
| gduggal-snapplat | SNP | * | map_l250_m1_e0 | het | 87.0994 | 83.6172 | 90.8842 | 94.6651 | 3976 | 779 | 3978 | 399 | 190 | 47.6190 | |
| ltrigg-rtg2 | SNP | * | map_l100_m0_e0 | * | 98.7191 | 97.6280 | 99.8350 | 53.7664 | 32062 | 779 | 32065 | 53 | 9 | 16.9811 | |
| gduggal-bwavard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 0.6378 | 0.0000 | 0.0000 | 5 | 779 | 0 | 0 | 0 | ||
| ghariani-varprowl | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 84.9840 | 84.8017 | 85.1670 | 81.2419 | 4341 | 778 | 4335 | 755 | 704 | 93.2450 | |
| gduggal-snapvard | INDEL | D16_PLUS | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 0.7653 | 0.0000 | 0.0000 | 6 | 778 | 0 | 0 | 0 | ||
| gduggal-snapvard | INDEL | D6_15 | HG002complexvar | homalt | 48.4509 | 33.4474 | 87.8641 | 42.5384 | 391 | 778 | 362 | 50 | 46 | 92.0000 | |
| anovak-vg | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 81.1375 | 80.9173 | 81.3588 | 37.8886 | 3299 | 778 | 3365 | 771 | 561 | 72.7626 | |
| anovak-vg | INDEL | D6_15 | HG002complexvar | het | 77.7392 | 75.0641 | 80.6119 | 50.1246 | 2342 | 778 | 2582 | 621 | 443 | 71.3366 | |
| jlack-gatk | INDEL | D6_15 | HG002compoundhet | hetalt | 94.7748 | 90.4552 | 99.5278 | 24.3596 | 7373 | 778 | 7377 | 35 | 30 | 85.7143 | |
| ckim-isaac | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 92.3980 | 87.5241 | 97.8468 | 61.7037 | 5458 | 778 | 5635 | 124 | 11 | 8.8710 | |
| ltrigg-rtg2 | SNP | ti | HG002complexvar | het | 99.8501 | 99.7528 | 99.9475 | 16.9710 | 313988 | 778 | 313992 | 165 | 46 | 27.8788 | |
| jmaeng-gatk | SNP | tv | map_l250_m1_e0 | het | 70.8070 | 56.4633 | 94.9200 | 96.9245 | 1009 | 778 | 1009 | 54 | 1 | 1.8519 | |
| gduggal-snapvard | SNP | tv | map_siren | het | 94.6657 | 97.2841 | 92.1846 | 72.3745 | 27832 | 777 | 27719 | 2350 | 198 | 8.4255 | |
| ckim-isaac | INDEL | * | map_l125_m2_e1 | * | 78.4183 | 65.0787 | 98.6367 | 88.3507 | 1448 | 777 | 1447 | 20 | 8 | 40.0000 | |