PrecisionFDA
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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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
3351-3400 / 86044 show all | |||||||||||||||
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 57.4755 | 62.1622 | 53.4460 | 78.1472 | 414 | 252 | 411 | 358 | 355 | 99.1620 | |
| jpowers-varprowl | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 57.4755 | 62.1622 | 53.4460 | 78.1472 | 414 | 252 | 411 | 358 | 355 | 99.1620 | |
| gduggal-snapvard | SNP | ti | map_siren | het | 95.3627 | 96.2088 | 94.5314 | 68.3335 | 60017 | 2365 | 59499 | 3442 | 355 | 10.3138 | |
| cchapple-custom | INDEL | I1_5 | * | * | 99.2924 | 98.8889 | 99.6992 | 56.2734 | 148990 | 1674 | 149480 | 451 | 355 | 78.7140 | |
| ckim-isaac | SNP | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 96.5147 | 94.2784 | 98.8597 | 54.0704 | 52448 | 3183 | 52797 | 609 | 355 | 58.2923 | |
| dgrover-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.3320 | 98.9618 | 97.7101 | 71.4422 | 17634 | 185 | 17239 | 404 | 355 | 87.8713 | |
| ckim-vqsr | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 98.2947 | 98.8383 | 97.7570 | 71.4388 | 17612 | 207 | 17215 | 395 | 354 | 89.6203 | |
| egarrison-hhga | INDEL | * | HG002complexvar | homalt | 98.5044 | 98.8604 | 98.1509 | 53.6323 | 26719 | 308 | 26700 | 503 | 354 | 70.3777 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 96.8947 | 98.7270 | 95.1293 | 53.9091 | 7290 | 94 | 7285 | 373 | 354 | 94.9062 | |
| qzeng-custom | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 88.4979 | 97.7029 | 80.8780 | 52.7675 | 638 | 15 | 2174 | 514 | 354 | 68.8716 | |
| jlack-gatk | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 92.4559 | 95.1485 | 89.9115 | 78.4139 | 3844 | 196 | 3556 | 399 | 354 | 88.7218 | |
| rpoplin-dv42 | INDEL | D1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 99.2133 | 99.5848 | 98.8446 | 73.6714 | 33098 | 138 | 33109 | 387 | 353 | 91.2145 | |
| jmaeng-gatk | INDEL | D6_15 | HG002compoundhet | * | 95.0402 | 94.1203 | 95.9783 | 36.0728 | 8500 | 531 | 8496 | 356 | 353 | 99.1573 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 97.7710 | 96.8925 | 98.6656 | 61.3340 | 30432 | 976 | 30464 | 412 | 353 | 85.6796 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 97.7710 | 96.8925 | 98.6656 | 61.3340 | 30432 | 976 | 30464 | 412 | 353 | 85.6796 | |
| mlin-fermikit | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 80.6298 | 89.3985 | 73.4276 | 74.6915 | 1189 | 141 | 1039 | 376 | 353 | 93.8830 | |
| ciseli-custom | SNP | ti | HG002complexvar | het | 96.3296 | 95.9112 | 96.7516 | 18.3708 | 301896 | 12870 | 299422 | 10053 | 353 | 3.5114 | |
| ghariani-varprowl | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 52.6126 | 49.5308 | 56.1033 | 72.8835 | 475 | 484 | 478 | 374 | 353 | 94.3850 | |
| gduggal-snapplat | SNP | tv | map_l125_m2_e1 | het | 93.3381 | 93.1962 | 93.4803 | 85.9836 | 9835 | 718 | 9836 | 686 | 353 | 51.4577 | |
| gduggal-snapfb | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 69.0921 | 61.2589 | 79.2222 | 54.8419 | 944 | 597 | 1426 | 374 | 353 | 94.3850 | |
| gduggal-snapplat | SNP | tv | map_l125_m2_e0 | het | 93.2998 | 93.1527 | 93.4473 | 85.9522 | 9727 | 715 | 9726 | 682 | 352 | 51.6129 | |
| rpoplin-dv42 | INDEL | * | lowcmp_SimpleRepeat_diTR_51to200 | * | 78.0896 | 75.1071 | 81.3187 | 71.3321 | 1578 | 523 | 1554 | 357 | 352 | 98.5994 | |
| qzeng-custom | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 83.3645 | 86.4174 | 80.5198 | 60.1495 | 2774 | 436 | 3005 | 727 | 352 | 48.4182 | |
| mlin-fermikit | INDEL | I1_5 | HG002complexvar | homalt | 96.8973 | 96.5125 | 97.2853 | 48.2881 | 12979 | 469 | 12901 | 360 | 351 | 97.5000 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 95.3085 | 94.9832 | 95.6360 | 75.7457 | 13840 | 731 | 13850 | 632 | 351 | 55.5380 | |
| mlin-fermikit | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 95.3085 | 94.9832 | 95.6360 | 75.7457 | 13840 | 731 | 13850 | 632 | 351 | 55.5380 | |
| mlin-fermikit | INDEL | D1_5 | HG002complexvar | het | 96.8827 | 95.7525 | 98.0399 | 50.2469 | 19883 | 882 | 19757 | 395 | 351 | 88.8608 | |
| ndellapenna-hhga | SNP | * | HG002complexvar | * | 99.7910 | 99.6474 | 99.9350 | 18.9550 | 751721 | 2660 | 751769 | 489 | 351 | 71.7791 | |
| gduggal-snapplat | SNP | tv | map_l125_m1_e0 | * | 93.2502 | 91.0465 | 95.5633 | 81.8317 | 14582 | 1434 | 14582 | 677 | 351 | 51.8464 | |
| gduggal-snapfb | SNP | ti | map_l150_m2_e1 | * | 96.3445 | 96.0141 | 96.6772 | 77.8313 | 19897 | 826 | 19901 | 684 | 351 | 51.3158 | |
| gduggal-bwafb | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | homalt | 92.8529 | 99.4937 | 87.0432 | 60.7107 | 2358 | 12 | 2358 | 351 | 351 | 100.0000 | |
| gduggal-bwaplat | SNP | tv | * | het | 98.5255 | 97.5640 | 99.5062 | 36.2003 | 577282 | 14414 | 577577 | 2866 | 351 | 12.2470 | |
| gduggal-bwafb | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt101bp_gt95identity_merged | * | 89.3164 | 86.6966 | 92.0994 | 71.2589 | 4438 | 681 | 4523 | 388 | 351 | 90.4639 | |
| hfeng-pmm3 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 97.4936 | 95.9940 | 99.0408 | 57.8182 | 41599 | 1736 | 41405 | 401 | 351 | 87.5312 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_51to200 | homalt | 42.6554 | 78.6458 | 29.2636 | 46.1940 | 151 | 41 | 151 | 365 | 351 | 96.1644 | |
| ciseli-custom | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 16.8236 | 10.3093 | 45.7020 | 62.4933 | 360 | 3132 | 319 | 379 | 351 | 92.6121 | |
| ckim-isaac | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 93.4046 | 90.2930 | 96.7382 | 47.0617 | 17934 | 1928 | 17795 | 600 | 351 | 58.5000 | |
| ciseli-custom | SNP | * | map_l250_m2_e1 | * | 69.2947 | 64.8053 | 74.4524 | 92.2088 | 5176 | 2811 | 5167 | 1773 | 350 | 19.7406 | |
| ckim-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 98.1904 | 98.9943 | 97.3994 | 67.4787 | 14470 | 147 | 14082 | 376 | 350 | 93.0851 | |
| hfeng-pmm1 | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 97.3761 | 95.8604 | 98.9406 | 51.0374 | 36333 | 1569 | 36144 | 387 | 350 | 90.4393 | |
| gduggal-snapplat | SNP | * | map_l150_m0_e0 | het | 89.5077 | 87.5441 | 91.5613 | 90.3664 | 6951 | 989 | 6955 | 641 | 350 | 54.6022 | |
| asubramanian-gatk | INDEL | I1_5 | HG002compoundhet | * | 95.2373 | 93.5902 | 96.9436 | 67.0365 | 11564 | 792 | 11577 | 365 | 350 | 95.8904 | |
| anovak-vg | SNP | tv | map_l150_m0_e0 | het | 76.3189 | 87.6187 | 67.6007 | 87.1885 | 2491 | 352 | 2485 | 1191 | 350 | 29.3871 | |
| qzeng-custom | SNP | ti | map_l100_m0_e0 | het | 81.5587 | 70.9290 | 95.9360 | 86.8580 | 9918 | 4065 | 9891 | 419 | 349 | 83.2936 | |
| qzeng-custom | SNP | ti | map_l150_m2_e0 | het | 80.5235 | 69.5753 | 95.5605 | 89.8900 | 8962 | 3919 | 8933 | 415 | 349 | 84.0964 | |
| qzeng-custom | SNP | ti | map_l150_m2_e1 | het | 80.5961 | 69.6581 | 95.6089 | 89.9144 | 9066 | 3949 | 9036 | 415 | 349 | 84.0964 | |
| gduggal-snapfb | SNP | ti | map_l150_m2_e0 | * | 96.3262 | 95.9877 | 96.6670 | 77.7511 | 19689 | 823 | 19693 | 679 | 349 | 51.3991 | |
| gduggal-snapfb | SNP | ti | map_l150_m1_e0 | * | 96.2042 | 95.8452 | 96.5660 | 76.1103 | 18893 | 819 | 18897 | 672 | 348 | 51.7857 | |
| anovak-vg | SNP | * | lowcmp_SimpleRepeat_diTR_11to50 | het | 90.7742 | 93.8101 | 87.9287 | 67.8048 | 5850 | 386 | 6359 | 873 | 348 | 39.8625 | |
| asubramanian-gatk | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_51to200bp_gt95identity_merged | * | 91.6951 | 91.4187 | 91.9731 | 70.0049 | 5561 | 522 | 5603 | 489 | 348 | 71.1656 | |