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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
21001-21050 / 86044 show all | |||||||||||||||
| asubramanian-gatk | SNP | ti | HG002compoundhet | hetalt | 95.8808 | 94.4732 | 97.3310 | 25.3652 | 547 | 32 | 547 | 15 | 0 | 0.0000 | |
| gduggal-bwafb | SNP | tv | * | * | 99.7254 | 99.8534 | 99.5978 | 25.3671 | 968276 | 1422 | 968379 | 3911 | 282 | 7.2104 | |
| qzeng-custom | SNP | tv | func_cds | homalt | 99.8531 | 99.7066 | 100.0000 | 25.3758 | 1699 | 5 | 1688 | 0 | 0 | ||
| raldana-dualsentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.1241 | 94.4089 | 100.0000 | 25.3923 | 6501 | 385 | 6514 | 0 | 0 | ||
| gduggal-snapvard | SNP | tv | HG002complexvar | het | 97.6940 | 97.1254 | 98.2693 | 25.4121 | 146401 | 4333 | 143709 | 2531 | 919 | 36.3098 | |
| ckim-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.2944 | 92.8778 | 99.9719 | 25.4138 | 3534 | 271 | 3559 | 1 | 1 | 100.0000 | |
| ghariani-varprowl | SNP | tv | HG002complexvar | homalt | 99.3856 | 99.9338 | 98.8434 | 25.4168 | 95048 | 63 | 95121 | 1113 | 736 | 66.1276 | |
| jmaeng-gatk | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_51to200 | hetalt | 94.6237 | 89.7959 | 100.0000 | 25.4237 | 44 | 5 | 44 | 0 | 0 | ||
| ckim-vqsr | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.2661 | 92.8252 | 99.9719 | 25.4244 | 3532 | 273 | 3557 | 1 | 1 | 100.0000 | |
| qzeng-custom | SNP | * | * | het | 99.4239 | 99.1899 | 99.6590 | 25.4299 | 1858423 | 15178 | 1850061 | 6331 | 818 | 12.9205 | |
| gduggal-bwavard | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 99.2943 | 98.5985 | 100.0000 | 25.4409 | 1407 | 20 | 1395 | 0 | 0 | ||
| jlack-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 94.3059 | 89.5985 | 99.5353 | 25.4660 | 7253 | 842 | 7283 | 34 | 30 | 88.2353 | |
| ndellapenna-hhga | INDEL | I6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 97.8885 | 97.4684 | 98.3122 | 25.4717 | 231 | 6 | 233 | 4 | 4 | 100.0000 | |
| gduggal-snapfb | SNP | tv | HG002complexvar | het | 98.4837 | 99.5363 | 97.4531 | 25.4817 | 150035 | 699 | 150338 | 3929 | 342 | 8.7045 | |
| gduggal-snapfb | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 85.2592 | 83.7329 | 86.8421 | 25.4902 | 489 | 95 | 66 | 10 | 10 | 100.0000 | |
| jlack-gatk | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 25.4919 | 1704 | 0 | 1704 | 0 | 0 | ||
| jli-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_51to200 | hetalt | 90.9027 | 83.6009 | 99.6021 | 25.4941 | 729 | 143 | 751 | 3 | 3 | 100.0000 | |
| asubramanian-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.6973 | 94.5364 | 98.9593 | 25.4960 | 6454 | 373 | 6466 | 68 | 64 | 94.1176 | |
| raldana-dualsentieon | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.6184 | 95.3476 | 100.0000 | 25.5017 | 5185 | 253 | 5197 | 0 | 0 | ||
| gduggal-bwaplat | SNP | tv | HG002complexvar | het | 97.0873 | 95.7892 | 98.4210 | 25.5027 | 144384 | 6347 | 144674 | 2321 | 283 | 12.1930 | |
| hfeng-pmm2 | SNP | * | func_cds | het | 99.8702 | 99.9731 | 99.7675 | 25.5047 | 11158 | 3 | 11155 | 26 | 0 | 0.0000 | |
| mlin-fermikit | INDEL | I1_5 | func_cds | * | 99.1690 | 99.4444 | 98.8950 | 25.5144 | 179 | 1 | 179 | 2 | 1 | 50.0000 | |
| ckim-isaac | INDEL | * | func_cds | homalt | 97.7376 | 95.5752 | 100.0000 | 25.5172 | 216 | 10 | 216 | 0 | 0 | ||
| ckim-isaac | SNP | tv | tech_badpromoters | homalt | 94.5946 | 89.7436 | 100.0000 | 25.5319 | 35 | 4 | 35 | 0 | 0 | ||
| hfeng-pmm2 | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.4702 | 95.0930 | 99.9692 | 25.5353 | 6492 | 335 | 6501 | 2 | 1 | 50.0000 | |
| hfeng-pmm3 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.7726 | 95.6622 | 99.9782 | 25.5368 | 4565 | 207 | 4577 | 1 | 0 | 0.0000 | |
| ckim-isaac | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 92.0493 | 86.2286 | 98.7126 | 25.5959 | 3281 | 524 | 3297 | 43 | 35 | 81.3953 | |
| jpowers-varprowl | SNP | tv | HG002complexvar | homalt | 99.4724 | 99.9411 | 99.0081 | 25.6082 | 95055 | 56 | 95130 | 953 | 743 | 77.9643 | |
| qzeng-custom | INDEL | I1_5 | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 25.6098 | 119 | 0 | 122 | 0 | 0 | ||
| ciseli-custom | SNP | * | func_cds | * | 97.9137 | 99.4601 | 96.4146 | 25.6110 | 18052 | 98 | 17990 | 669 | 42 | 6.2780 | |
| ltrigg-rtg1 | INDEL | I1_5 | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 25.6250 | 119 | 0 | 119 | 0 | 0 | ||
| rpoplin-dv42 | SNP | * | func_cds | het | 99.9149 | 99.9462 | 99.8836 | 25.6262 | 11155 | 6 | 11152 | 13 | 3 | 23.0769 | |
| ckim-isaac | SNP | ti | lowcmp_SimpleRepeat_triTR_11to50 | het | 97.8866 | 96.2470 | 99.5832 | 25.6355 | 2385 | 93 | 2389 | 10 | 0 | 0.0000 | |
| raldana-dualsentieon | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 95.6668 | 91.6936 | 100.0000 | 25.6384 | 4261 | 386 | 4310 | 0 | 0 | ||
| jmaeng-gatk | INDEL | I1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.0820 | 92.4836 | 99.9718 | 25.6399 | 3519 | 286 | 3543 | 1 | 1 | 100.0000 | |
| astatham-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.6772 | 96.0184 | 99.3942 | 25.6555 | 4582 | 190 | 4594 | 28 | 27 | 96.4286 | |
| hfeng-pmm3 | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 96.9697 | 94.1176 | 100.0000 | 25.6765 | 3792 | 237 | 3818 | 0 | 0 | ||
| ltrigg-rtg1 | INDEL | D6_15 | HG002compoundhet | hetalt | 96.2297 | 93.1910 | 99.4731 | 25.6779 | 7596 | 555 | 7552 | 40 | 40 | 100.0000 | |
| mlin-fermikit | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 77.3563 | 63.1748 | 99.7477 | 25.6850 | 5114 | 2981 | 5140 | 13 | 13 | 100.0000 | |
| bgallagher-sentieon | INDEL | D1_5 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 96.8780 | 94.3944 | 99.4959 | 25.6896 | 6500 | 386 | 6513 | 33 | 33 | 100.0000 | |
| hfeng-pmm1 | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 98.1326 | 96.3537 | 99.9783 | 25.7249 | 4598 | 174 | 4610 | 1 | 0 | 0.0000 | |
| eyeh-varpipe | SNP | * | HG002complexvar | hetalt | 99.7172 | 99.6774 | 99.7570 | 25.7273 | 309 | 1 | 6978 | 17 | 16 | 94.1176 | |
| astatham-gatk | INDEL | D1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt101bp_gt95identity_merged | hetalt | 96.9440 | 94.4163 | 99.6108 | 25.7275 | 7643 | 452 | 7678 | 30 | 29 | 96.6667 | |
| ltrigg-rtg2 | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | hetalt | 99.5701 | 99.1438 | 100.0000 | 25.7325 | 579 | 5 | 583 | 0 | 0 | ||
| ltrigg-rtg2 | SNP | tv | func_cds | homalt | 100.0000 | 100.0000 | 100.0000 | 25.7516 | 1704 | 0 | 1704 | 0 | 0 | ||
| astatham-gatk | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRlt7_lt51bp_gt95identity_merged | hetalt | 97.4954 | 95.1601 | 99.9482 | 25.7593 | 3834 | 195 | 3860 | 2 | 2 | 100.0000 | |
| gduggal-snapvard | SNP | ti | * | het | 98.9307 | 98.9471 | 98.9142 | 25.7701 | 1268399 | 13497 | 1263991 | 13875 | 2046 | 14.7459 | |
| dgrover-gatk | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 97.7426 | 96.1442 | 99.3950 | 25.7739 | 4588 | 184 | 4600 | 28 | 27 | 96.4286 | |
| ckim-gatk | SNP | tv | func_cds | homalt | 99.8236 | 99.6479 | 100.0000 | 25.7867 | 1698 | 6 | 1698 | 0 | 0 | ||
| rpoplin-dv42 | INDEL | D6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | hetalt | 95.9098 | 92.6401 | 99.4187 | 25.8018 | 6646 | 528 | 6670 | 39 | 38 | 97.4359 | |