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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
85251-85300 / 86044 show all | |||||||||||||||
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 55.3475 | 87.7323 | 40.4253 | 50.7774 | 3304 | 462 | 3289 | 4847 | 4536 | 93.5837 | |
| ciseli-custom | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 55.3475 | 87.7323 | 40.4253 | 50.7774 | 3304 | 462 | 3289 | 4847 | 4536 | 93.5837 | |
| gduggal-snapvard | SNP | * | map_l100_m2_e0 | het | 93.3360 | 96.7693 | 90.1379 | 78.6381 | 44900 | 1499 | 44319 | 4849 | 371 | 7.6511 | |
| ghariani-varprowl | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 73.9195 | 72.9786 | 74.8850 | 67.4004 | 14495 | 5367 | 14485 | 4858 | 4633 | 95.3685 | |
| gduggal-snapvard | INDEL | D6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 59.1721 | 54.4401 | 64.8052 | 53.7673 | 8736 | 7311 | 8947 | 4859 | 4228 | 87.0138 | |
| ndellapenna-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 86.7164 | 95.8976 | 79.1397 | 59.1322 | 17088 | 731 | 18434 | 4859 | 4632 | 95.3283 | |
| gduggal-bwavard | INDEL | I6_15 | HG002compoundhet | het | 6.3867 | 74.0385 | 3.3373 | 37.4814 | 154 | 54 | 168 | 4866 | 4788 | 98.3970 | |
| gduggal-bwavard | INDEL | I6_15 | HG002compoundhet | * | 2.5796 | 2.0283 | 3.5425 | 37.8475 | 178 | 8598 | 179 | 4874 | 4796 | 98.3997 | |
| gduggal-snapvard | SNP | * | map_l100_m2_e1 | het | 93.3754 | 96.7973 | 90.1872 | 78.6618 | 45396 | 1502 | 44805 | 4875 | 376 | 7.7128 | |
| gduggal-snapvard | SNP | * | map_l100_m1_e0 | * | 94.9349 | 96.5402 | 93.3822 | 73.4477 | 69898 | 2505 | 68917 | 4884 | 410 | 8.3948 | |
| gduggal-snapplat | INDEL | I1_5 | HG002complexvar | * | 77.0714 | 71.7352 | 83.2654 | 65.6966 | 23933 | 9430 | 24301 | 4884 | 375 | 7.6781 | |
| gduggal-snapvard | SNP | * | map_l100_m2_e0 | * | 95.0024 | 96.5659 | 93.4887 | 74.9387 | 71424 | 2540 | 70426 | 4905 | 414 | 8.4404 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 87.8643 | 91.4147 | 84.5794 | 78.5110 | 26247 | 2465 | 26903 | 4905 | 1242 | 25.3211 | |
| anovak-vg | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 87.8643 | 91.4147 | 84.5794 | 78.5110 | 26247 | 2465 | 26903 | 4905 | 1242 | 25.3211 | |
| gduggal-snapfb | SNP | ti | HG002compoundhet | het | 78.4798 | 97.2856 | 65.7667 | 46.9249 | 9247 | 258 | 9427 | 4907 | 174 | 3.5460 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | het | 84.4168 | 96.1004 | 75.2662 | 52.8425 | 14047 | 570 | 14984 | 4924 | 4785 | 97.1771 | |
| gduggal-snapvard | SNP | * | map_l100_m2_e1 | * | 95.0240 | 96.5773 | 93.5198 | 74.9627 | 72179 | 2558 | 71162 | 4931 | 419 | 8.4973 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 91.3695 | 99.3801 | 84.5540 | 81.4321 | 28534 | 178 | 27026 | 4937 | 134 | 2.7142 | |
| eyeh-varpipe | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 91.3695 | 99.3801 | 84.5540 | 81.4321 | 28534 | 178 | 27026 | 4937 | 134 | 2.7142 | |
| jlack-gatk | SNP | * | map_siren | het | 97.0812 | 99.4593 | 94.8142 | 68.9379 | 90499 | 492 | 90485 | 4949 | 324 | 6.5468 | |
| jlack-gatk | INDEL | * | * | * | 98.6899 | 98.8138 | 98.5664 | 60.1151 | 340455 | 4087 | 340332 | 4950 | 2708 | 54.7071 | |
| gduggal-snapfb | SNP | tv | HG002complexvar | * | 98.7938 | 99.5787 | 98.0211 | 25.3464 | 245118 | 1037 | 245440 | 4955 | 529 | 10.6761 | |
| qzeng-custom | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 96.3917 | 97.6114 | 95.2022 | 68.9543 | 47118 | 1153 | 98539 | 4966 | 2712 | 54.6114 | |
| jpowers-varprowl | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 38.7027 | 35.8682 | 42.0236 | 64.3849 | 3613 | 6460 | 3601 | 4968 | 4896 | 98.5507 | |
| jlack-gatk | SNP | * | map_siren | * | 98.0143 | 99.3920 | 96.6743 | 64.0744 | 145339 | 889 | 145316 | 4999 | 358 | 7.1614 | |
| egarrison-hhga | INDEL | * | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 94.1721 | 98.0713 | 90.5711 | 70.5632 | 47340 | 931 | 48307 | 5029 | 4714 | 93.7363 | |
| gduggal-bwavard | SNP | tv | * | het | 99.1377 | 99.1291 | 99.1462 | 30.0519 | 586551 | 5153 | 584089 | 5030 | 1454 | 28.9066 | |
| eyeh-varpipe | INDEL | D1_5 | * | * | 95.6258 | 94.7617 | 96.5059 | 56.5047 | 139058 | 7687 | 139038 | 5034 | 4747 | 94.2988 | |
| ghariani-varprowl | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | het | 56.3707 | 87.9455 | 41.4787 | 65.8135 | 3553 | 487 | 3568 | 5034 | 4915 | 97.6361 | |
| gduggal-bwafb | SNP | ti | * | het | 99.7363 | 99.8649 | 99.6080 | 22.2231 | 1280165 | 1732 | 1280284 | 5038 | 382 | 7.5824 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 69.0793 | 87.2712 | 57.1635 | 56.5737 | 2146 | 313 | 6735 | 5047 | 4364 | 86.4672 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | het | 87.9422 | 91.6371 | 84.5336 | 63.1509 | 27931 | 2549 | 27596 | 5049 | 4851 | 96.0784 | |
| mlin-fermikit | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | het | 87.9422 | 91.6371 | 84.5336 | 63.1509 | 27931 | 2549 | 27596 | 5049 | 4851 | 96.0784 | |
| egarrison-hhga | INDEL | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | het | 86.2517 | 96.2231 | 78.1528 | 59.6097 | 17146 | 673 | 18083 | 5055 | 4861 | 96.1622 | |
| gduggal-snapvard | INDEL | D1_5 | HG002complexvar | * | 89.5567 | 91.9115 | 87.3195 | 53.8184 | 30067 | 2646 | 34830 | 5058 | 3634 | 71.8466 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 60.1668 | 61.4104 | 58.9725 | 57.4072 | 5164 | 3245 | 7289 | 5071 | 4386 | 86.4918 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 93.8037 | 98.1533 | 89.8233 | 81.9505 | 44858 | 844 | 44997 | 5098 | 525 | 10.2982 | |
| jpowers-varprowl | SNP | * | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 93.8037 | 98.1533 | 89.8233 | 81.9505 | 44858 | 844 | 44997 | 5098 | 525 | 10.2982 | |
| jpowers-varprowl | INDEL | I1_5 | HG002compoundhet | het | 20.5402 | 73.6471 | 11.9344 | 70.4320 | 626 | 224 | 691 | 5099 | 5074 | 99.5097 | |
| gduggal-snapfb | INDEL | * | HG002complexvar | * | 90.4920 | 87.9994 | 93.1300 | 55.3026 | 67705 | 9233 | 69298 | 5112 | 2371 | 46.3811 | |
| gduggal-snapfb | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | * | 35.0458 | 95.2883 | 21.4714 | 85.0675 | 1355 | 67 | 1398 | 5113 | 85 | 1.6624 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 70.2572 | 87.5000 | 58.6914 | 56.3300 | 7315 | 1045 | 7266 | 5114 | 4566 | 89.2843 | |
| ciseli-custom | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 70.2572 | 87.5000 | 58.6914 | 56.3300 | 7315 | 1045 | 7266 | 5114 | 4566 | 89.2843 | |
| gduggal-snapplat | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | het | 37.4948 | 41.7896 | 34.0005 | 84.4865 | 2550 | 3552 | 2650 | 5144 | 58 | 1.1275 | |
| mlin-fermikit | SNP | * | HG002complexvar | homalt | 98.3225 | 98.4247 | 98.2205 | 20.7847 | 284029 | 4546 | 284043 | 5146 | 4990 | 96.9685 | |
| ciseli-custom | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 45.1864 | 43.7705 | 46.6970 | 66.0012 | 4409 | 5664 | 4517 | 5156 | 3623 | 70.2676 | |
| gduggal-snapvard | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | het | 75.4653 | 90.5356 | 64.6962 | 41.2162 | 1234 | 129 | 9456 | 5160 | 4823 | 93.4690 | |
| gduggal-bwavard | SNP | tv | * | * | 99.2324 | 99.0032 | 99.4627 | 26.1679 | 960032 | 9666 | 955309 | 5161 | 1540 | 29.8392 | |
| gduggal-bwaplat | SNP | ti | HG002complexvar | het | 97.7064 | 97.0801 | 98.3410 | 19.6959 | 305575 | 9191 | 306161 | 5165 | 589 | 11.4037 | |
| ghariani-varprowl | INDEL | * | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 43.5285 | 42.1324 | 45.0202 | 75.7921 | 4244 | 5829 | 4231 | 5167 | 5021 | 97.1744 | |