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 | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
73851-73900 / 86044 show all | |||||||||||||||
| gduggal-snapfb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 0.0000 | 0.0000 | 0.0000 | 0 | 205 | 0 | 0 | 0 | |||
| gduggal-snapfb | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 0.0000 | 0.0000 | 0.0000 | 0 | 205 | 0 | 0 | 0 | |||
| gduggal-snapplat | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | homalt | 0.0000 | 0.0000 | 0.0000 | 0 | 205 | 0 | 0 | 0 | |||
| gduggal-snapplat | INDEL | I16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | homalt | 0.0000 | 0.0000 | 0.0000 | 0 | 205 | 0 | 0 | 0 | |||
| cchapple-custom | INDEL | D6_15 | lowcmp_SimpleRepeat_diTR_11to50 | hetalt | 0.0000 | 95.7041 | 0.0000 | 0.0000 | 4567 | 205 | 0 | 0 | 0 | ||
| ckim-vqsr | SNP | ti | segdup | homalt | 98.5954 | 97.2685 | 99.9589 | 88.0169 | 7300 | 205 | 7300 | 3 | 3 | 100.0000 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 98.9598 | 98.5931 | 99.3293 | 80.6409 | 14366 | 205 | 14366 | 97 | 14 | 14.4330 | |
| ckim-vqsr | SNP | tv | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 98.9598 | 98.5931 | 99.3293 | 80.6409 | 14366 | 205 | 14366 | 97 | 14 | 14.4330 | |
| egarrison-hhga | SNP | tv | map_l100_m2_e1 | * | 99.4981 | 99.1892 | 99.8090 | 65.1604 | 25078 | 205 | 25078 | 48 | 19 | 39.5833 | |
| ckim-vqsr | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | * | 99.3204 | 98.9679 | 99.6754 | 59.9358 | 19657 | 205 | 19650 | 64 | 45 | 70.3125 | |
| egarrison-hhga | INDEL | D1_5 | lowcmp_SimpleRepeat_triTR_11to50 | * | 95.1579 | 94.9718 | 95.3448 | 39.6821 | 3872 | 205 | 3871 | 189 | 179 | 94.7090 | |
| gduggal-bwafb | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | homalt | 95.7062 | 94.1759 | 97.2870 | 68.5937 | 3331 | 206 | 3335 | 93 | 84 | 90.3226 | |
| gduggal-snapfb | INDEL | * | map_l100_m2_e1 | het | 92.9455 | 91.2079 | 94.7505 | 82.9512 | 2137 | 206 | 2184 | 121 | 22 | 18.1818 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | hetalt | 96.9769 | 94.1577 | 99.9702 | 43.4270 | 3320 | 206 | 3360 | 1 | 1 | 100.0000 | |
| hfeng-pmm2 | INDEL | I6_15 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | hetalt | 96.9769 | 94.1577 | 99.9702 | 43.4270 | 3320 | 206 | 3360 | 1 | 1 | 100.0000 | |
| jlack-gatk | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_gt95identity_merged | * | 95.1732 | 94.9348 | 95.4128 | 68.8499 | 3861 | 206 | 3848 | 185 | 153 | 82.7027 | |
| raldana-dualsentieon | SNP | ti | map_l125_m2_e0 | het | 98.7385 | 98.9087 | 98.5689 | 73.7413 | 18670 | 206 | 18666 | 271 | 3 | 1.1070 | |
| raldana-dualsentieon | SNP | ti | map_l125_m2_e1 | het | 98.7395 | 98.9207 | 98.5590 | 73.8046 | 18881 | 206 | 18877 | 276 | 3 | 1.0870 | |
| asubramanian-gatk | SNP | * | lowcmp_SimpleRepeat_homopolymer_6to10 | * | 99.2719 | 98.8007 | 99.7476 | 56.4979 | 16971 | 206 | 16992 | 43 | 6 | 13.9535 | |
| anovak-vg | INDEL | D6_15 | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 65.0593 | 53.4989 | 82.9932 | 36.5011 | 237 | 206 | 244 | 50 | 34 | 68.0000 | |
| asubramanian-gatk | INDEL | * | map_l150_m2_e1 | * | 90.1401 | 85.6845 | 95.0845 | 97.7994 | 1233 | 206 | 1238 | 64 | 7 | 10.9375 | |
| mlin-fermikit | SNP | ti | lowcmp_SimpleRepeat_quadTR_11to50 | * | 98.3740 | 98.0805 | 98.6692 | 39.1607 | 10526 | 206 | 10528 | 142 | 102 | 71.8310 | |
| ciseli-custom | INDEL | * | map_l100_m0_e0 | homalt | 66.3988 | 59.5285 | 75.0617 | 86.5938 | 303 | 206 | 304 | 101 | 79 | 78.2178 | |
| ltrigg-rtg1 | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | * | 97.7403 | 96.1234 | 99.4126 | 61.0480 | 5108 | 206 | 5077 | 30 | 17 | 56.6667 | |
| ltrigg-rtg1 | INDEL | I1_5 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 98.0884 | 96.5308 | 99.6971 | 74.3115 | 5732 | 206 | 5924 | 18 | 18 | 100.0000 | |
| jli-custom | SNP | * | map_l250_m2_e0 | * | 98.2912 | 97.3874 | 99.2119 | 86.5904 | 7679 | 206 | 7679 | 61 | 30 | 49.1803 | |
| jpowers-varprowl | SNP | * | map_l150_m1_e0 | homalt | 98.9052 | 98.1726 | 99.6488 | 74.4202 | 11067 | 206 | 11067 | 39 | 26 | 66.6667 | |
| jpowers-varprowl | SNP | ti | map_siren | homalt | 99.6196 | 99.4567 | 99.7830 | 54.0684 | 37710 | 206 | 37711 | 82 | 57 | 69.5122 | |
| gduggal-snapplat | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 0.0000 | 0.0000 | 0.0000 | 0 | 206 | 0 | 0 | 0 | |||
| ghariani-varprowl | SNP | * | map_l250_m2_e1 | * | 95.6014 | 97.4208 | 93.8488 | 91.4722 | 7781 | 206 | 7781 | 510 | 89 | 17.4510 | |
| gduggal-snapfb | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 0.0000 | 0.0000 | 0.0000 | 0 | 206 | 0 | 0 | 0 | |||
| gduggal-snapvard | INDEL | I16_PLUS | lowcmp_AllRepeats_51to200bp_gt95identity_merged | * | 0.0000 | 0.0000 | 25.0000 | 67.1429 | 0 | 206 | 23 | 69 | 23 | 33.3333 | |
| gduggal-snapfb | INDEL | I1_5 | lowcmp_SimpleRepeat_quadTR_11to50 | het | 75.9768 | 87.8450 | 66.9339 | 67.8314 | 1496 | 207 | 1670 | 825 | 122 | 14.7879 | |
| gduggal-snapplat | SNP | tv | map_l250_m0_e0 | * | 81.2227 | 72.9412 | 91.6256 | 96.8509 | 558 | 207 | 558 | 51 | 14 | 27.4510 | |
| ghariani-varprowl | SNP | ti | HG002complexvar | hetalt | 0.0000 | 0.0000 | 0.0000 | 0 | 207 | 0 | 0 | 0 | |||
| 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 | |
| jlack-gatk | INDEL | I6_15 | lowcmp_AllRepeats_lt51bp_gt95identity_merged | hetalt | 96.5213 | 93.3654 | 99.8981 | 44.6324 | 2913 | 207 | 2942 | 3 | 3 | 100.0000 | |
| jlack-gatk | SNP | ti | map_l100_m2_e1 | homalt | 99.3913 | 98.8807 | 99.9071 | 60.0864 | 18287 | 207 | 18287 | 17 | 15 | 88.2353 | |
| hfeng-pmm2 | INDEL | * | lowcmp_SimpleRepeat_quadTR_11to50 | het | 98.9153 | 98.1365 | 99.7066 | 60.6969 | 10901 | 207 | 10875 | 32 | 10 | 31.2500 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331 | * | 96.8438 | 95.8592 | 97.8488 | 71.3186 | 4792 | 207 | 4776 | 105 | 68 | 64.7619 | |
| hfeng-pmm1 | INDEL | D16_PLUS | lowcmp_Human_Full_Genome_TRDB_hg19_150331_all_merged | * | 96.8438 | 95.8592 | 97.8488 | 71.3186 | 4792 | 207 | 4776 | 105 | 68 | 64.7619 | |
| 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 | |
| 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 | |
| gduggal-bwavard | SNP | tv | lowcmp_SimpleRepeat_diTR_11to50 | * | 95.8975 | 95.7372 | 96.0584 | 69.6019 | 4649 | 207 | 4606 | 189 | 80 | 42.3280 | |
| gduggal-snapfb | INDEL | * | lowcmp_SimpleRepeat_triTR_11to50 | homalt | 92.5726 | 90.3810 | 94.8730 | 43.3628 | 1945 | 207 | 1943 | 105 | 74 | 70.4762 | |
| gduggal-bwaplat | INDEL | D6_15 | lowcmp_SimpleRepeat_quadTR_11to50 | homalt | 85.3906 | 75.6471 | 98.0153 | 59.9388 | 643 | 207 | 642 | 13 | 11 | 84.6154 | |
| gduggal-bwaplat | INDEL | I1_5 | lowcmp_Human_Full_Genome_TRDB_hg19_150331_TRgt6_lt51bp_gt95identity_merged | het | 76.2512 | 62.2951 | 98.2659 | 87.5405 | 342 | 207 | 340 | 6 | 1 | 16.6667 | |
| gduggal-bwafb | INDEL | D16_PLUS | lowcmp_SimpleRepeat_quadTR_11to50 | * | 85.7428 | 78.4150 | 94.5813 | 55.1133 | 752 | 207 | 768 | 44 | 43 | 97.7273 | |
| gduggal-bwaplat | INDEL | * | lowcmp_SimpleRepeat_homopolymer_6to10 | hetalt | 75.6632 | 61.3084 | 98.7952 | 82.4710 | 328 | 207 | 328 | 4 | 4 | 100.0000 | |
| gduggal-bwaplat | INDEL | D1_5 | map_l100_m2_e0 | homalt | 79.4494 | 66.1211 | 99.5074 | 87.9739 | 404 | 207 | 404 | 2 | 1 | 50.0000 | |